From shimoyama at mcw.edu Fri Jun 1 10:19:41 2007 From: shimoyama at mcw.edu (Shimoyama, Mary) Date: Fri Jun 1 12:48:25 2007 Subject: [rat-forum] RGD NEW RELEASE - New data for rat genes Message-ID: <1448A38A42714048B9C53E473E13CCF0CA61D8@davis.hmgc.mcw.edu> ANNOUNCING NEW RGD RELEASE RGD is happy to announce its 3rd major release of 2007. This release includes the addition of Celera genome positions for genes Celera Genome Positions RGD now provides genomic positions for genes on the Celera Assembly http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=3876 as well as a Celera Assembly option on the GBrowse to provide users with a view of data elements within the context of the Celera Assembly. New Protein Links Weekly updates of data from the International Protein Index now provide users with the most up to date links to essential protein and family information and identifiers including IPI, UNIPARC, Ensembl Protein, InterPro, Pfam, PRINTS, PROSITE, PANTHER, RZPD, SMART, ProDom, Superfamily-SCOP, TIGRFAM, and Gene3D-Cath. (http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=621533) Disease Genes The Rat orthologs of 1547 genes listed at OMIM have been fully curated using all rat papers published on each gene. Gene Families and Nomenclature The nomenclature for two major gene families, alpha tubulin and prolactin related genes has been completed. Identification and nomenclature assignment was coordinated with Dr. Michael Soares and the Mouse Genome Database. Details were published in Soares et al, Mammalian Genome 2007, Mar 18(3):154-6 http://rgd.mcw.edu/tools/references/references_view.cgi?id=1624237 A publication on the nomenclature resolution of the alpha tubulin family will appear in Genomics soon. Mary Shimoyama Program Manager Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin shimoyama@mcw.edu Tel: 414-456-7505 Fax: 414-456-6595 http://rgd.mcw.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070601/ede5c42c/attachment-0001.html From shimoyama at mcw.edu Fri Jun 1 10:23:20 2007 From: shimoyama at mcw.edu (Shimoyama, Mary) Date: Fri Jun 1 12:49:07 2007 Subject: [rat-forum] RGD NEW RELEASE - New Ortholog Data Message-ID: <1448A38A42714048B9C53E473E13CCF0CA61D9@davis.hmgc.mcw.edu> ANNOUNCING NEW RGD RELEASE RGD is happy to announce its 3rd major release of 2007. This release includes the addition major developments in ortholog data and ortholog map information. Human and Mouse Genes Weekly downloads from EntrezGene now provide RGD users with up-to-date, complete data on human and mouse genes including: * Genomic and cytogenetic map positions * Summary description paragraphs for human genes and some mouse genes http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=1344192 * Links to GDB, MGD, KEGG, Uniprot, PubMed, HGNC, NPRD, EntrezGene, UniGene, OMIM * Links to human and mouse genes in UCSC Browser and NCBI MapView * Links to nucleotide and protein sequences * Links to GEO for expression data * Links to PubMed references * Gene searches for any or all species are available through the general search or gene query form Orthology Data Ortholog relationships among rat, mouse and human are now updated weekly. Comparative map data for all three species are provided on each gene report as well as a link to the comparative map at NCBI Map Viewer. Mary Shimoyama Program Manager Rat Genome Database Human and Molecular Genetics Center Medical College of Wisconsin shimoyama@mcw.edu Tel: 414-456-7505 Fax: 414-456-6595 http://rgd.mcw.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070601/1c949e16/attachment.html From phz at ethz.ch Mon Jun 4 08:21:08 2007 From: phz at ethz.ch (Philip Zimmermann) Date: Tue Jun 5 08:37:57 2007 Subject: [rat-forum] Housekeeping genes for RT-PCR Message-ID: <466411C4.5090705@ethz.ch> Dear Robert, We recently looked for genes that have minimal variance throughout a large set of microarrays. For rat, this was done by querying the set of rat 31K Affymetrix arrays from the Genevestigator database. We think to have found several good candidates, or at least they seem to perform better in the microarray data than many classically used control genes like b-actin. Here are three candidates from the low, medium and high expression range: LOW: probe set: 1367921_at gene name: Ilkap RGD link: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=620128 MEDIUM: probe set: 1389245_at gene name: Psmd7_predicted RGD link: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=1306902 HIGH: probe set: 1398843_at gene name: Vapa RGD link: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=61803 In the attached image you will see their profiles across 748 arrays (the image was generated with the "Northern" tool from Genevestigator). Hope this helps. If you happen to choose any of these as controls for your experiments, it would be interesting to know whether they met your expectations or not. Perhaps RT-PCR would need control genes identified using the same technology rather than microarrays to be most reproducible, but I am not aware if this hypothesis has ever been tested. Best regards, Philip -- ETH Zurich Dr. Philip Zimmermann Genevestigator / Bioinformatics Universit?tsstrasse 2 8092 Zurich, Switzerland phz@ethz.ch http://www.pb.ethz.ch https://www.genevestigator.ethz.ch +41 44 632 67 32 (phone office) -------------- next part -------------- A non-text attachment was scrubbed... Name: rat_housekeeping.png Type: image/png Size: 194654 bytes Desc: not available Url : http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070604/c3940faf/rat_housekeeping-0001.png From dongbing75 at hotmail.com Sun Jun 3 02:35:02 2007 From: dongbing75 at hotmail.com (dong bing) Date: Tue Jun 5 09:34:05 2007 Subject: [rat-forum] RE: rat-forum Digest, Vol 3, Issue 1 Message-ID: Let me clarify it: We need to collect blood from E20 fetuses when rat dams are killed and fetuses are taken out as cesarian described. E20 fetuses are so small to me... then how to collect blood to assay hormone level etc in terms of tools and procedures? Bing Please clarify. Do you mean other than doing a cesarian section and decapitating the E20 fetuses? HR dong bing wrote: > Hi guys,> > Good to find this forum by google hunting to ask rat-related > questions in lab experiments.> > We designed an experiment to acquire blood from embryonic rat (20 > gestation days). Could you please supply with methods? Thanks> > Bing>> ------------------------------------------------------------------------> Change is good. See what's different about Windows Live Hotmail. Check > it out! ************************************************ Bing Dong dongbing75@hotmail.com > From: rat-forum-request@mcw.edu> Subject: rat-forum Digest, Vol 3, Issue 1> To: rat-forum@mcw.edu> Date: Fri, 1 Jun 2007 12:48:47 -0500> > Send rat-forum mailing list submissions to> rat-forum@mcw.edu> > To subscribe or unsubscribe via the World Wide Web, visit> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum> or, via email, send a message with subject or body 'help' to> rat-forum-request@mcw.edu> > You can reach the person managing the list at> rat-forum-owner@mcw.edu> > When replying, please edit your Subject line so it is more specific> than "Re: Contents of rat-forum digest..."> > > Rat Community Forum DIGEST of messages> > Today's Topics:> > 1. Freezing rat sperm (Ron Korstanje)> 2. how to acquire rat embryo blood (dong bing)> 3. Re: how to acquire rat embryo blood (Hershel Raff)> 4. RE: Freezing rat sperm (Birger Voigt)> 5. Re: Housekeeping genes for RT-PCR (Bruce McCallum)> 6. Genevestigator releases rat expression data (Philip Zimmermann)> 7. RGD NEW RELEASE - New data for rat genes (Shimoyama, Mary)> > > ----------------------------------------------------------------------> > Message: 1> Date: Tue, 15 May 2007 04:54:57 +0200> From: Ron Korstanje > Subject: [rat-forum] Freezing rat sperm> To: > Message-ID: > Content-Type: text/plain; charset="US-ASCII"> > Dear forum,> > We would like to freeze rat sperm from two lines and send it abroad to have> it assayed on oocyte binding capability (we suspect differences between the> lines).> However, I have heard from various sources that frozen rat sperm is not> capable of binding anymore.> > Is this true, or are there protocols that might be successful?> > thanks,> > Ron> > > Ron Korstanje, PhD > > University Medical Center Groningen> Medical Biology division> Hanzeplein 1 > 9713 GZ Groningen > The Netherlands > phone: +31-50 3635777> email: r.korstanje@med.umcg.nl> > > > > > ------------------------------> > Message: 2> Date: Thu, 17 May 2007 01:15:21 -0400> From: dong bing > Subject: [rat-forum] how to acquire rat embryo blood> To: > Message-ID: > Content-Type: text/plain; charset="iso-8859-1"> > Hi guys,> > Good to find this forum by google hunting to ask rat-related questions in lab experiments. > > We designed an experiment to acquire blood from embryonic rat (20 gestation days). Could you please supply with methods? Thanks> > Bing> _________________________________________________________________> Add some color. Personalize your inbox with your favorite colors.> www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0507> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070517/e56a14e1/attachment-0001.html> > ------------------------------> > Message: 3> Date: Thu, 17 May 2007 09:05:05 -0500> From: Hershel Raff > Subject: Re: [rat-forum] how to acquire rat embryo blood> To: Rat Community Forum > Message-ID: <464C6111.6070008@mcw.edu>> Content-Type: text/plain; charset="us-ascii"> > Please clarify. Do you mean other than doing a cesarian section and > decapitating the E20 fetuses? HR> > dong bing wrote:> > > Hi guys,> > > > Good to find this forum by google hunting to ask rat-related > > questions in lab experiments.> > > > We designed an experiment to acquire blood from embryonic rat (20 > > gestation days). Could you please supply with methods? Thanks> > > > Bing> >> > ------------------------------------------------------------------------> > Change is good. See what's different about Windows Live Hotmail. Check > > it out! > > > >> >> >------------------------------------------------------------------------> >> >_______________________________________________> >rat-forum mailing list> >rat-forum@mcw.edu> >http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum> > > >> -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070517/b9308adb/attachment-0001.html> > ------------------------------> > Message: 4> Date: Fri, 18 May 2007 09:43:40 +0900> From: "Birger Voigt" > Subject: RE: [rat-forum] Freezing rat sperm> To: "Rat Community Forum" > Message-ID:> <4D963D0E0320AD4BA7B54D58BC9A89D442E0B3@mail.anim.med.kyoto-u.ac.jp>> Content-Type: text/plain; charset="us-ascii"> > Hello Ron,> There are several protocols for in-vitro-fertilization using frozen sperms. I> think they would not be able of fertilizing any ovum in case they would had> lost their binding capability.> We are currently preparing a DVD manual in English for several> cryopreservation methods in the rat that includes also protocols for sperm> freezing. If you are interested, please contact me directly.> Regards,> Birger Voigt> > > Birger Voigt, PhD> Institute of Laboratory Animals> Graduate School of Medicine> Kyoto University> Sakyo-ku> Kyoto, 606-8501> Japan> Tel.: +81 75 753 9318> Fax.: +81 75 753 4409> e-mail: birger@anim.med.kyoto-u.ac.jp> HP: www.anim.med.kyoto-u.ac.jp/NBR > > > > -----Original Message-----> From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf> Of Ron Korstanje> Sent: Dienstag, 15. Mai 2007 11:55> To: rat-forum@mcw.edu> Subject: [rat-forum] Freezing rat sperm> > Dear forum,> > We would like to freeze rat sperm from two lines and send it abroad to have> it assayed on oocyte binding capability (we suspect differences between the> lines).> However, I have heard from various sources that frozen rat sperm is not> capable of binding anymore.> > Is this true, or are there protocols that might be successful?> > thanks,> > Ron> > > Ron Korstanje, PhD > > University Medical Center Groningen> Medical Biology division> Hanzeplein 1 > 9713 GZ Groningen > The Netherlands > phone: +31-50 3635777> email: r.korstanje@med.umcg.nl> > > > _______________________________________________> rat-forum mailing list> rat-forum@mcw.edu> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum> > > ------------------------------> > Message: 5> Date: Tue, 22 May 2007 19:08:45 -0500> From: Bruce McCallum > Subject: Re: [rat-forum] Housekeeping genes for RT-PCR> To: Rat Community Forum > Message-ID: <9628D745-3FAF-43A7-9185-A74F00415B0C@mcw.edu>> Content-Type: text/plain; charset="us-ascii"> > George,> Is it possible to forward a digital copy of the Biotechniques > article? The April issue is stuck deep in the bowels of the > circulation department, and our library does not subscribe to the > digital service.> Thanks,> -bmc> On Apr 24, 2007, at 3:11 PM, George Cicila wrote:> > > Robert,> > There was a recent article in Biotechniques by Hong et al. > > [Biotechniques 42(4):503-512. 2007] that deals with your question. > > They conducted a microarray and qRT-PCR study, and recommend > > control genes for 11 rat tissues (unfortunately not pancreas).> >> > George Cicila> >> >> > On 4/24/07 3:10 PM, "Robert Wallis" wrote:> >> >> Dear rat forum subscribers> >>> >> We are trying to find a suitable housekeeping gene to normalise to > >> using real time pcr (at the moment we are looking in the > >> pancreas). We are presently having 'issues' with beta actin; > >> similar sized bands appear from both genomic and cDNA, even though > >> designed over an exon-exon boundary, with 3 different designs of > >> primers plus a commercially available one, (who mentioned it may > >> be due to an extra pseudogene, giving the excuse that the rat > >> sequence is not as well validated as it's mouse and human > >> counterparts)> >>> >> Suffice to say; has anyone had similar issues regarding > >> housekeeping genes in the rat, and have you any advice on which > >> housekeeping genes to use, and perhaps more importantly which to > >> avoid?> >>> >> Many Thanks> >>> >>> >> Robert Wallis> >>> >> Sunnybrook Research Institute> >> Division of Molecular and Cell Biology> >> 2075 Bayview Avenue; RM A3-31> >> Toronto> >> Ontario> >> M4N 3M5> >> CANADA> >>> >> Tel; 416 480 6100 xt 7297 (lab) xt 7293 (office)> >>> >>> >>> >>> >>> >> _______________________________________________> >> rat-forum mailing list> >> rat-forum@mcw.edu> >> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum> >> > _______________________________________________> > rat-forum mailing list> > rat-forum@mcw.edu> > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum> > J. Bruce McCallum> Research Scientist> Department of Anesthesiology, M4340> Medical College of Wisconsin> 8701 Watertown Plank Rd.> Milwaukee, WI 53226> Phone: (414)456-5682> FAX: (414)456-6507> > > > -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070522/640d5248/attachment-0001.html> > ------------------------------> > Message: 6> Date: Thu, 31 May 2007 15:26:48 +0200> From: Philip Zimmermann > Subject: [rat-forum] Genevestigator releases rat expression data> To: rat-forum@mcw.edu> Message-ID: <465ECD18.5080705@ethz.ch>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed> > Dear All,> > The Swiss Federal Institute of Technology Zurich (ETH Zurich) has > recently released a new version of Genevestigator, a popular expression > meta-analysis tool previously containing only mouse and arabidopsis > data. The new version now contains 2894 quality-controlled and curated > rat microarrays from 94 public experiments. Many of these experiments > are from toxicogenomics.> > Genevestigator was designed by biologists, developed by software > engineers, and is user-friendly with biologists as end-users in mind. > The classical tools allow users to look at how genes are expressed in > many different tissues, developmental stages, stimuli, drug treatments, > diseases, and genetic modifications. More recently developed advanced > tools additionally allow to search for biomarkers, cluster genes with > similar meta-profiles, and project expression data onto metabolic > networks (mouse and arabidopsis).> > The classical tools are freely available for academic users. Just be > sure you have Java 1.4.2 or higher on your computer to run the analysis > tool. Genevestigator can be found at:> https://www.genevestigator.ethz.ch> > Some screenshots are available here:> https://www.genevestigator.ethz.ch/index.php?option=com_content&task=view&id=49> > The tools might be of interest to molecular biologists and scientists > working in toxicogenomics and diagnostics.> > Philip Zimmermann, ETH Zurich, Switzerland> > -- > ETH Zurich> Dr. Philip Zimmermann> Genevestigator / Bioinformatics> Universit?tsstrasse 2> 8092 Zurich, Switzerland> > phz@ethz.ch> http://www.pb.ethz.ch> https://www.genevestigator.ethz.ch> +41 44 632 67 32 (phone office)> > > > ------------------------------> > Message: 7> Date: Fri, 1 Jun 2007 10:19:41 -0500> From: "Shimoyama, Mary" > Subject: [rat-forum] RGD NEW RELEASE - New data for rat genes> To: > Message-ID:> <1448A38A42714048B9C53E473E13CCF0CA61D8@davis.hmgc.mcw.edu>> Content-Type: text/plain; charset="us-ascii"> > ANNOUNCING NEW RGD RELEASE > > RGD is happy to announce its 3rd major release of 2007. This release> includes the addition of Celera genome positions for genes> > > > Celera Genome Positions> > RGD now provides genomic positions for genes on the Celera Assembly> http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=3876> > as well as a Celera Assembly option on the GBrowse to provide users with> a view of data elements within the context of the Celera Assembly. > > > > New Protein Links> > Weekly updates of data from the International Protein Index now provide> users with the most up to date links to essential protein and family> information and identifiers including IPI, UNIPARC, Ensembl Protein,> InterPro, Pfam, PRINTS, PROSITE, PANTHER, RZPD, SMART, ProDom,> Superfamily-SCOP, TIGRFAM, and Gene3D-Cath.> (http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=621533)> > > > Disease Genes> > The Rat orthologs of 1547 genes listed at OMIM have been fully curated> using all rat papers published on each gene.> > > > Gene Families and Nomenclature> > The nomenclature for two major gene families, alpha tubulin and> prolactin related genes has been completed. Identification and> nomenclature assignment was coordinated with Dr. Michael Soares and the> Mouse Genome Database. Details were published in Soares et al,> Mammalian Genome 2007, Mar 18(3):154-6> http://rgd.mcw.edu/tools/references/references_view.cgi?id=1624237 A> publication on the nomenclature resolution of the alpha tubulin family> will appear in Genomics soon.> > > > > > Mary Shimoyama> > Program Manager> > Rat Genome Database> > Human and Molecular Genetics Center> > Medical College of Wisconsin> > shimoyama@mcw.edu> > Tel: 414-456-7505> > Fax: 414-456-6595> > http://rgd.mcw.edu> > > > > > -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070601/ede5c42c/attachment.html> > ------------------------------> > _______________________________________________> rat-forum mailing list> rat-forum@mcw.edu> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum> > > End of rat-forum Digest, Vol 3, Issue 1> *************************************** _________________________________________________________________ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070603/17519ed4/attachment-0001.html From paulas at pobox.upenn.edu Tue Jun 5 13:38:34 2007 From: paulas at pobox.upenn.edu (Paula A. Clifford) Date: Tue Jun 5 13:43:38 2007 Subject: [rat-forum] IV injection in neonatal mice In-Reply-To: References: Message-ID: <6.2.5.6.2.20070605143629.01e421d0@pobox.upenn.edu> Can someone share your technique for IV injection (50ul) in neonatal (1-2) day old C57BL/6 mice. Thank you, Paula Paula Samalonis Clifford, BA, LVT, RLATG Training Manager University Laboratory Animal Resources University of Pennsylvania 3800 Spruce Street, Suite 177E Philadelphia, PA 19104 p: 215-898-2432 f: 215-573-9998 paulas@pobox.upenn.edu From AMAYER at midwestern.edu Tue Jun 5 13:54:08 2007 From: AMAYER at midwestern.edu (Mayer, Alejandro) Date: Tue Jun 5 14:00:57 2007 Subject: [rat-forum] Anesthesia young rats Message-ID: <1C4C481AB565DC42A3A9AB1986C29CF549D985@ildgmail1.midwestern.edu> I am interested in a method to anesthetize neonatal rats (postnatal day 5-7). If a reference is available that would be very helpful. Thanks, Alex Alejandro M.S. Mayer, Ph.D. Professor of Pharmacology Department of Pharmacology, CCOM Midwestern University 555 31st Street Downers Grove, Illinois 60515, USA Phone (630) 515-6951 Fax (630) 515-6295 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070605/4bf0db68/attachment.html From mabba2 at email.uky.edu Tue Jun 5 14:05:34 2007 From: mabba2 at email.uky.edu (Abbassi, Maggie) Date: Tue Jun 5 14:08:22 2007 Subject: [rat-forum] Anesthesia young rats In-Reply-To: <1C4C481AB565DC42A3A9AB1986C29CF549D985@ildgmail1.midwestern.edu> References: <1C4C481AB565DC42A3A9AB1986C29CF549D985@ildgmail1.midwestern.edu> Message-ID: I have used isoflurane inhalational anesthesia along with placing the rats on a cooling block after induction to synergize the anesthetic effect. Maggie Abbassi Graduate Student University of Kentucky ________________________________ From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of Mayer, Alejandro Sent: Tuesday, June 05, 2007 2:54 PM To: rat-forum@mcw.edu Subject: [rat-forum] Anesthesia young rats I am interested in a method to anesthetize neonatal rats (postnatal day 5-7). If a reference is available that would be very helpful. Thanks, Alex Alejandro M.S. Mayer, Ph.D. Professor of Pharmacology Department of Pharmacology, CCOM Midwestern University 555 31st Street Downers Grove, Illinois 60515, USA Phone (630) 515-6951 Fax (630) 515-6295 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070605/97c00f6c/attachment.html From cwscouten at myneurolab.com Tue Jun 5 14:10:40 2007 From: cwscouten at myneurolab.com (Charles Scouten) Date: Tue Jun 5 14:20:12 2007 Subject: [rat-forum] Anesthesia young rats References: <1C4C481AB565DC42A3A9AB1986C29CF549D985@ildgmail1.midwestern.edu> Message-ID: <5784D843593D874C93E9BADCB87342AB035073D9@tpiserver03.Coretech-holdings.com> See the references at the bottom of the product page link below: http://www.myneurolab.com/myneurolab/mnl_products_detail.asp?idproduct=4 62954&catdesc=Surgical+Equipment&CatThreeID=38&CatOneID=2&subcatdesc=Ste reotaxic+Instruments&idsubcategory=4 Two are favorable to hypothermia anesthetization, one finds long term changes. Cordially, Charles W. Scouten, Ph.D. President, myNeuroLab.com 5918 Evergreen Blvd. St. Louis, MO 63134 Ph: 314 522 0300 x 342 FAX 314 522 0377 cwscouten@myneurolab.com http://www.myneurolab.com ________________________________ From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of Mayer, Alejandro Sent: Tuesday, June 05, 2007 1:54 PM To: rat-forum@mcw.edu Subject: [rat-forum] Anesthesia young rats I am interested in a method to anesthetize neonatal rats (postnatal day 5-7). If a reference is available that would be very helpful. Thanks, Alex Alejandro M.S. Mayer, Ph.D. Professor of Pharmacology Department of Pharmacology, CCOM Midwestern University 555 31st Street Downers Grove, Illinois 60515, USA Phone (630) 515-6951 Fax (630) 515-6295 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070605/54419707/attachment.html From AMAYER at midwestern.edu Tue Jun 5 14:11:13 2007 From: AMAYER at midwestern.edu (Mayer, Alejandro) Date: Tue Jun 5 14:20:48 2007 Subject: [rat-forum] Anesthesia young rats In-Reply-To: Message-ID: <1C4C481AB565DC42A3A9AB1986C29CF549D986@ildgmail1.midwestern.edu> Maggie, thanks for the prompt response. Do you happen to know of a reference for the method? If so, thanks, Alex Alejandro M.S. Mayer, Ph.D. Professor of Pharmacology Department of Pharmacology, CCOM Midwestern University 555 31st Street Downers Grove, Illinois 60515, USA Phone (630) 515-6951 Fax (630) 515-6295 ________________________________ From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of Abbassi, Maggie Sent: Tuesday, June 05, 2007 2:06 PM To: Rat Community Forum Subject: RE: [rat-forum] Anesthesia young rats I have used isoflurane inhalational anesthesia along with placing the rats on a cooling block after induction to synergize the anesthetic effect. Maggie Abbassi Graduate Student University of Kentucky ________________________________ From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of Mayer, Alejandro Sent: Tuesday, June 05, 2007 2:54 PM To: rat-forum@mcw.edu Subject: [rat-forum] Anesthesia young rats I am interested in a method to anesthetize neonatal rats (postnatal day 5-7). If a reference is available that would be very helpful. Thanks, Alex Alejandro M.S. Mayer, Ph.D. Professor of Pharmacology Department of Pharmacology, CCOM Midwestern University 555 31st Street Downers Grove, Illinois 60515, USA Phone (630) 515-6951 Fax (630) 515-6295 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070605/a0b10c6c/attachment-0001.html From mabba2 at email.uky.edu Tue Jun 5 14:23:52 2007 From: mabba2 at email.uky.edu (Abbassi, Maggie) Date: Tue Jun 5 14:30:50 2007 Subject: [rat-forum] Anesthesia young rats In-Reply-To: <1C4C481AB565DC42A3A9AB1986C29CF549D986@ildgmail1.midwestern.edu> References: <1C4C481AB565DC42A3A9AB1986C29CF549D986@ildgmail1.midwestern.edu> Message-ID: Dr. Mayer, Unfortunately I don't have any. It was by trial and error. My studies are terminal so I am not concerned about long term effects. Maggie ________________________________ From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of Mayer, Alejandro Sent: Tuesday, June 05, 2007 3:11 PM To: Rat Community Forum Subject: RE: [rat-forum] Anesthesia young rats Maggie, thanks for the prompt response. Do you happen to know of a reference for the method? If so, thanks, Alex Alejandro M.S. Mayer, Ph.D. Professor of Pharmacology Department of Pharmacology, CCOM Midwestern University 555 31st Street Downers Grove, Illinois 60515, USA Phone (630) 515-6951 Fax (630) 515-6295 ________________________________ From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of Abbassi, Maggie Sent: Tuesday, June 05, 2007 2:06 PM To: Rat Community Forum Subject: RE: [rat-forum] Anesthesia young rats I have used isoflurane inhalational anesthesia along with placing the rats on a cooling block after induction to synergize the anesthetic effect. Maggie Abbassi Graduate Student University of Kentucky ________________________________ From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of Mayer, Alejandro Sent: Tuesday, June 05, 2007 2:54 PM To: rat-forum@mcw.edu Subject: [rat-forum] Anesthesia young rats I am interested in a method to anesthetize neonatal rats (postnatal day 5-7). If a reference is available that would be very helpful. Thanks, Alex Alejandro M.S. Mayer, Ph.D. Professor of Pharmacology Department of Pharmacology, CCOM Midwestern University 555 31st Street Downers Grove, Illinois 60515, USA Phone (630) 515-6951 Fax (630) 515-6295 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070605/3181bb58/attachment.html From azuniga at mcw.edu Tue Jun 5 15:41:16 2007 From: azuniga at mcw.edu (Zuniga-Meyer, Angela) Date: Tue Jun 5 15:42:02 2007 Subject: [rat-forum] Posted on Behalf of Ensembl - Ensembl hands-on courses Message-ID: <1448A38A42714048B9C53E473E13CCF09E1744@davis.hmgc.mcw.edu> Posted on Behalf of Ensembl- Hi guys, Re: Ensembl hands-on courses. We are looking at trying to combine a number of mid-west (US) locations for our Outreach people to visit. We normally give a 1 day, hands-on course, tailored to the institute, which we have good feedback about their effectiveness. We regularly do courses around Europe (about twice a month). We'd like to get 3 or 4 locations (or more, if there is demand) to visit. The institutions would share the travel costs, but we would not otherwise charge for the course. Could interested people contact Xose (xose@ebi.ac.uk) for more details. At some point, we'd also be interested in running an East Coast and Asian tour - if there were people interested in courses - indeed from anywhere - we'd like to hear from you. Please do forward this message to institutes or people you think might be interested. Ewan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070605/ad978088/attachment.html From webpresence at verizon.net Tue Jun 5 15:55:23 2007 From: webpresence at verizon.net (Web Presence) Date: Tue Jun 5 15:56:57 2007 Subject: @CHECK [rat-forum] Posted on Behalf of Ensembl - Ensembl hands-on courses References: <1448A38A42714048B9C53E473E13CCF09E1744@davis.hmgc.mcw.edu> Message-ID: <001c01c7a7b3$d6acec70$660fa8c0@atlas> Please let us know when an east coast tour is scheduled. Thanks! ----- Original Message ----- From: Zuniga-Meyer, Angela To: rat-forum@mcw.edu Sent: Tuesday, June 05, 2007 15:41 Subject: @CHECK [rat-forum] Posted on Behalf of Ensembl - Ensembl hands-on courses Posted on Behalf of Ensembl- Hi guys, Re: Ensembl hands-on courses. We are looking at trying to combine a number of mid-west (US) locations for our Outreach people to visit. We normally give a 1 day, hands-on course, tailored to the institute, which we have good feedback about their effectiveness. We regularly do courses around Europe (about twice a month). We'd like to get 3 or 4 locations (or more, if there is demand) to visit. The institutions would share the travel costs, but we would not otherwise charge for the course. Could interested people contact Xose (xose@ebi.ac.uk) for more details. At some point, we'd also be interested in running an East Coast and Asian tour - if there were people interested in courses - indeed from anywhere - we'd like to hear from you. Please do forward this message to institutes or people you think might be interested. Ewan ------------------------------------------------------------------------------ _______________________________________________ rat-forum mailing list rat-forum@mcw.edu http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum ------------------------------------------------------------------------------ No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.446 / Virus Database: 269.8.7/830 - Release Date: 6/3/2007 12:47 PM -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070605/1627cd8e/attachment-0001.html From e-redei at northwestern.edu Mon Jun 11 10:06:55 2007 From: e-redei at northwestern.edu (Eva E. Redei) Date: Mon Jun 11 10:04:13 2007 Subject: [rat-forum] RE: rat-forum Digest, Vol 3, Issue 1 In-Reply-To: References: Message-ID: <7.0.1.0.2.20070611100525.037d2a50@northwestern.edu> You need to use capillary tubes preferably heparinized. Eva At 02:35 AM 6/3/2007, you wrote: >Let me clarify it: > >We need to collect blood from E20 fetuses when >rat dams are killed and fetuses are taken out as >cesarian described. E20 fetuses are so small to >me... then how to collect blood to assay hormone >level etc in terms of tools and procedures? > >Bing > > >Please clarify. Do you mean other than doing a cesarian section and >decapitating the E20 fetuses? HR > >dong bing wrote: > > > Hi guys, > > > > Good to find this forum by google hunting to ask rat-related > > questions in lab experiments. > > > > We designed an experiment to acquire blood from embryonic rat (20 > > gestation days). Could you please supply with methods? Thanks > > > > Bing > > > > ------------------------------------------------------------------------ > > Change is good. See what's different about Windows Live Hotmail. Check > > it out! > > >************************************************ >Bing Dong >dongbing75@hotmail.com > > >---------- > > From: rat-forum-request@mcw.edu > > Subject: rat-forum Digest, Vol 3, Issue 1 > > To: rat-forum@mcw.edu > > Date: Fri, 1 Jun 2007 12:48:47 -0500 > > > > Send rat-forum mailing list submissions to > > rat-forum@mcw.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > or, via email, send a message with subject or body 'help' to > > rat-forum-request@mcw.edu > > > > You can reach the person managing the list at > > rat-forum-owner@mcw.edu > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of rat-forum digest..." > > > > > > Rat Community Forum DIGEST of messages > > > > Today's Topics: > > > > 1. Freezing rat sperm (Ron Korstanje) > > 2. how to acquire rat embryo blood (dong bing) > > 3. Re: how to acquire rat embryo blood (Hershel Raff) > > 4. RE: Freezing rat sperm (Birger Voigt) > > 5. Re: Housekeeping genes for RT-PCR (Bruce McCallum) > > 6. Genevestigator releases rat expression data (Philip Zimmermann) > > 7. RGD NEW RELEASE - New data for rat genes (Shimoyama, Mary) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 15 May 2007 04:54:57 +0200 > > From: Ron Korstanje > > Subject: [rat-forum] Freezing rat sperm > > To: > > Message-ID: > > Content-Type: text/plain; charset="US-ASCII" > > > > Dear forum, > > > > We would like to freeze rat sperm from two lines and send it abroad to have > > it assayed on oocyte binding capability (we suspect differences between the > > lines). > > However, I have heard from various sources that frozen rat sperm is not > > capable of binding anymore. > > > > Is this true, or are there protocols that might be successful? > > > > thanks, > > > > Ron > > > > > > Ron Korstanje, PhD > > > > University Medical Center Groningen > > Medical Biology division > > Hanzeplein 1 > > 9713 GZ Groningen > > The Netherlands > > phone: +31-50 3635777 > > email: r.korstanje@med.umcg.nl > > > > > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 17 May 2007 01:15:21 -0400 > > From: dong bing > > Subject: [rat-forum] how to acquire rat embryo blood > > To: > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi guys, > > > > Good to find this forum by google hunting to > ask rat-related questions in lab experiments. > > > > We designed an experiment to acquire blood > from embryonic rat (20 gestation days). Could > you please supply with methods? Thanks > > > > Bing > > _________________________________________________________________ > > Add some color. Personalize your inbox with your favorite colors. > > > www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0507 > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070517/e56a14e1/attachment-0001.html > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 17 May 2007 09:05:05 -0500 > > From: Hershel Raff > > Subject: Re: [rat-forum] how to acquire rat embryo blood > > To: Rat Community Forum > > Message-ID: <464C6111.6070008@mcw.edu> > > Content-Type: text/plain; charset="us-ascii" > > > > Please clarify. Do you mean other than doing a cesarian section and > > decapitating the E20 fetuses? HR > > > > dong bing wrote: > > > > > Hi guys, > > > > > > Good to find this forum by google hunting to ask rat-related > > > questions in lab experiments. > > > > > > We designed an experiment to acquire blood from embryonic rat (20 > > > gestation days). Could you please supply with methods? Thanks > > > > > > Bing > > > > > > ------------------------------------------------------------------------ > > > Change is good. See what's different about Windows Live Hotmail. Check > > > it out! > > > > > > > > > > > > > >------------------------------------------------------------------------ > > > > > >_______________________________________________ > > >rat-forum mailing list > > >rat-forum@mcw.edu > > >http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070517/b9308adb/attachment-0001.html > > > > ------------------------------ > > > > Message: 4 > > Date: Fri, 18 May 2007 09:43:40 +0900 > > From: "Birger Voigt" > > Subject: RE: [rat-forum] Freezing rat sperm > > To: "Rat Community Forum" > > Message-ID: > > <4D963D0E0320AD4BA7B54D58BC9A89D442E0B3@mail.anim.med.kyoto-u.ac.jp> > > Content-Type: text/plain; charset="us-ascii" > > > > Hello Ron, > > There are several protocols for > in-vitro-fertilization using frozen sperms. I > > think they would not be able of fertilizing any ovum in case they would had > > lost their binding capability. > > We are currently preparing a DVD manual in English for several > > cryopreservation methods in the rat that includes also protocols for sperm > > freezing. If you are interested, please contact me directly. > > Regards, > > Birger Voigt > > > > > > Birger Voigt, PhD > > Institute of Laboratory Animals > > Graduate School of Medicine > > Kyoto University > > Sakyo-ku > > Kyoto, 606-8501 > > Japan > > Tel.: +81 75 753 9318 > > Fax.: +81 75 753 4409 > > e-mail: birger@anim.med.kyoto-u.ac.jp > > HP: www.anim.med.kyoto-u.ac.jp/NBR > > > > > > > > -----Original Message----- > > From: rat-forum-bounces@mcw.edu > [mailto:rat-forum-bounces@mcw.edu] On Behalf > > Of Ron Korstanje > > Sent: Dienstag, 15. Mai 2007 11:55 > > To: rat-forum@mcw.edu > > Subject: [rat-forum] Freezing rat sperm > > > > Dear forum, > > > > We would like to freeze rat sperm from two lines and send it abroad to have > > it assayed on oocyte binding capability (we suspect differences between the > > lines). > > However, I have heard from various sources that frozen rat sperm is not > > capable of binding anymore. > > > > Is this true, or are there protocols that might be successful? > > > > thanks, > > > > Ron > > > > > > Ron Korstanje, PhD > > > > University Medical Center Groningen > > Medical Biology division > > Hanzeplein 1 > > 9713 GZ Groningen > > The Netherlands > > phone: +31-50 3635777 > > email: r.korstanje@med.umcg.nl > > > > > > > > _______________________________________________ > > rat-forum mailing list > > rat-forum@mcw.edu > > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 22 May 2007 19:08:45 -0500 > > From: Bruce McCallum > > Subject: Re: [rat-forum] Housekeeping genes for RT-PCR > > To: Rat Community Forum > > Message-ID: <9628D745-3FAF-43A7-9185-A74F00415B0C@mcw.edu> > > Content-Type: text/plain; charset="us-ascii" > > > > George, > > Is it possible to forward a digital copy of the Biotechniques > > article? The April issue is stuck deep in the bowels of the > > circulation department, and our library does not subscribe to the > > digital service. > > Thanks, > > -bmc > > On Apr 24, 2007, at 3:11 PM, George Cicila wrote: > > > > > Robert, > > > There was a recent article in Biotechniques by Hong et al. > > > [Biotechniques 42(4):503-512. 2007] that deals with your question. > > > They conducted a microarray and qRT-PCR study, and recommend > > > control genes for 11 rat tissues (unfortunately not pancreas). > > > > > > George Cicila > > > > > > > > > On 4/24/07 3:10 PM, "Robert Wallis" wrote: > > > > > >> Dear rat forum subscribers > > >> > > >> We are trying to find a suitable housekeeping gene to normalise to > > >> using real time pcr (at the moment we are looking in the > > >> pancreas). We are presently having 'issues' with beta actin; > > >> similar sized bands appear from both genomic and cDNA, even though > > >> designed over an exon-exon boundary, with 3 different designs of > > >> primers plus a commercially available one, (who mentioned it may > > >> be due to an extra pseudogene, giving the excuse that the rat > > >> sequence is not as well validated as it's mouse and human > > >> counterparts) > > >> > > >> Suffice to say; has anyone had similar issues regarding > > >> housekeeping genes in the rat, and have you any advice on which > > >> housekeeping genes to use, and perhaps more importantly which to > > >> avoid? > > >> > > >> Many Thanks > > >> > > >> > > >> Robert Wallis > > >> > > >> Sunnybrook Research Institute > > >> Division of Molecular and Cell Biology > > >> 2075 Bayview Avenue; RM A3-31 > > >> Toronto > > >> Ontario > > >> M4N 3M5 > > >> CANADA > > >> > > >> Tel; 416 480 6100 xt 7297 (lab) xt 7293 (office) > > >> > > >> > > >> > > >> > > >> > > >> _______________________________________________ > > >> rat-forum mailing list > > >> rat-forum@mcw.edu > > >> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > > > > > _______________________________________________ > > > rat-forum mailing list > > > rat-forum@mcw.edu > > > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > > > J. Bruce McCallum > > Research Scientist > > Department of Anesthesiology, M4340 > > Medical College of Wisconsin > > 8701 Watertown Plank Rd. > > Milwaukee, WI 53226 > > Phone: (414)456-5682 > > FAX: (414)456-6507 > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070522/640d5248/attachment-0001.html > > > > ------------------------------ > > > > Message: 6 > > Date: Thu, 31 May 2007 15:26:48 +0200 > > From: Philip Zimmermann > > Subject: [rat-forum] Genevestigator releases rat expression data > > To: rat-forum@mcw.edu > > Message-ID: <465ECD18.5080705@ethz.ch> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Dear All, > > > > The Swiss Federal Institute of Technology Zurich (ETH Zurich) has > > recently released a new version of Genevestigator, a popular expression > > meta-analysis tool previously containing only mouse and arabidopsis > > data. The new version now contains 2894 quality-controlled and curated > > rat microarrays from 94 public experiments. Many of these experiments > > are from toxicogenomics. > > > > Genevestigator was designed by biologists, developed by software > > engineers, and is user-friendly with biologists as end-users in mind. > > The classical tools allow users to look at how genes are expressed in > > many different tissues, developmental stages, stimuli, drug treatments, > > diseases, and genetic modifications. More recently developed advanced > > tools additionally allow to search for biomarkers, cluster genes with > > similar meta-profiles, and project expression data onto metabolic > > networks (mouse and arabidopsis). > > > > The classical tools are freely available for academic users. Just be > > sure you have Java 1.4.2 or higher on your computer to run the analysis > > tool. Genevestigator can be found at: > > https://www.genevestigator.ethz.ch > > > > Some screenshots are available here: > > > https://www.genevestigator.ethz.ch/index.php?option=com_content&task=view&id=49 > > > > The tools might be of interest to molecular biologists and scientists > > working in toxicogenomics and diagnostics. > > > > Philip Zimmermann, ETH Zurich, Switzerland > > > > -- > > ETH Zurich > > Dr. Philip Zimmermann > > Genevestigator / Bioinformatics > > Universit?tsstrasse 2 > > 8092 Zurich, Switzerland > > > > phz@ethz.ch > > http://www.pb.ethz.ch > > https://www.genevestigator.ethz.ch > > +41 44 632 67 32 (phone office) > > > > > > > > ------------------------------ > > > > Message: 7 > > Date: Fri, 1 Jun 2007 10:19:41 -0500 > > From: "Shimoyama, Mary" > > Subject: [rat-forum] RGD NEW RELEASE - New data for rat genes > > To: > > Message-ID: > > <1448A38A42714048B9C53E473E13CCF0CA61D8@davis.hmgc.mcw.edu> > > Content-Type: text/plain; charset="us-ascii" > > > > ANNOUNCING NEW RGD RELEASE > > > > RGD is happy to announce its 3rd major release of 2007. This release > > includes the addition of Celera genome positions for genes > > > > > > > > Celera Genome Positions > > > > RGD now provides genomic positions for genes on the Celera Assembly > > http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=3876 > > > > as well as a Celera Assembly option on the GBrowse to provide users with > > a view of data elements within the context of the Celera Assembly. > > > > > > > > New Protein Links > > > > Weekly updates of data from the International Protein Index now provide > > users with the most up to date links to essential protein and family > > information and identifiers including IPI, UNIPARC, Ensembl Protein, > > InterPro, Pfam, PRINTS, PROSITE, PANTHER, RZPD, SMART, ProDom, > > Superfamily-SCOP, TIGRFAM, and Gene3D-Cath. > > (http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=621533) > > > > > > > > Disease Genes > > > > The Rat orthologs of 1547 genes listed at OMIM have been fully curated > > using all rat papers published on each gene. > > > > > > > > Gene Families and Nomenclature > > > > The nomenclature for two major gene families, alpha tubulin and > > prolactin related genes has been completed. Identification and > > nomenclature assignment was coordinated with Dr. Michael Soares and the > > Mouse Genome Database. Details were published in Soares et al, > > Mammalian Genome 2007, Mar 18(3):154-6 > > http://rgd.mcw.edu/tools/references/references_view.cgi?id=1624237 A > > publication on the nomenclature resolution of the alpha tubulin family > > will appear in Genomics soon. > > > > > > > > > > > > Mary Shimoyama > > > > Program Manager > > > > Rat Genome Database > > > > Human and Molecular Genetics Center > > > > Medical College of Wisconsin > > > > shimoyama@mcw.edu > > > > Tel: 414-456-7505 > > > > Fax: 414-456-6595 > > > > http://rgd.mcw.edu > > > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070601/ede5c42c/attachment.html > > > > ------------------------------ > > > > _______________________________________________ > > rat-forum mailing list > > rat-forum@mcw.edu > > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > > > > > End of rat-forum Digest, Vol 3, Issue 1 > > *************************************** > > >---------- >Change is good. See what's different about >Windows Live Hotmail. >Check it out! >_______________________________________________ >rat-forum mailing list >rat-forum@mcw.edu >http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070611/9cc47c3c/attachment-0001.html From hraff at mcw.edu Mon Jun 11 10:15:09 2007 From: hraff at mcw.edu (Hershel Raff) Date: Mon Jun 11 10:18:31 2007 Subject: [rat-forum] RE: rat-forum Digest, Vol 3, Issue 1 In-Reply-To: <7.0.1.0.2.20070611100525.037d2a50@northwestern.edu> References: <7.0.1.0.2.20070611100525.037d2a50@northwestern.edu> Message-ID: <466D66FD.3030502@mcw.edu> You can also use Capiject tubes (Terumo) Lithium Heparin Ref: T-MLH. (They can be purchased through Fisher). These are terrific mini-tubes that are used in drawing blood from human babies all the time. We routinely use these when we decapitate neonates/fetuses - they also come with EDTA and other preservatives. They are a LOT easier to use than capillary tubes. HR Eva E. Redei wrote: > You need to use capillary tubes preferably heparinized. > > Eva > > At 02:35 AM 6/3/2007, you wrote: > >> Let me clarify it: >> >> We need to collect blood from E20 fetuses when rat dams are killed >> and fetuses are taken out as cesarian described. E20 fetuses are so >> small to me... then how to collect blood to assay hormone level etc >> in terms of tools and procedures? >> >> Bing >> >> >> Please clarify. Do you mean other than doing a cesarian section and >> decapitating the E20 fetuses? HR >> >> dong bing wrote: >> >> > Hi guys, >> > >> > Good to find this forum by google hunting to ask rat-related >> > questions in lab experiments. >> > >> > We designed an experiment to acquire blood from embryonic rat (20 >> > gestation days). Could you please supply with methods? Thanks >> > >> > Bing >> > >> > >> ------------------------------------------------------------------------ >> > Change is good. See what's different about Windows Live Hotmail. Check >> > it out! >> >> >> ************************************************ >> Bing Dong >> dongbing75@hotmail.com >> >> ------------------------------------------------------------------------ >> > From: rat-forum-request@mcw.edu >> > Subject: rat-forum Digest, Vol 3, Issue 1 >> > To: rat-forum@mcw.edu >> > Date: Fri, 1 Jun 2007 12:48:47 -0500 >> > >> > Send rat-forum mailing list submissions to >> > rat-forum@mcw.edu >> > >> > To subscribe or unsubscribe via the World Wide Web, visit >> > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum >> > or, via email, send a message with subject or body 'help' to >> > rat-forum-request@mcw.edu >> > >> > You can reach the person managing the list at >> > rat-forum-owner@mcw.edu >> > >> > When replying, please edit your Subject line so it is more specific >> > than "Re: Contents of rat-forum digest..." >> > >> > >> > Rat Community Forum DIGEST of messages >> > >> > Today's Topics: >> > >> > 1. Freezing rat sperm (Ron Korstanje) >> > 2. how to acquire rat embryo blood (dong bing) >> > 3. Re: how to acquire rat embryo blood (Hershel Raff) >> > 4. RE: Freezing rat sperm (Birger Voigt) >> > 5. Re: Housekeeping genes for RT-PCR (Bruce McCallum) >> > 6. Genevestigator releases rat expression data (Philip Zimmermann) >> > 7. RGD NEW RELEASE - New data for rat genes (Shimoyama, Mary) >> > >> > >> > ---------------------------------------------------------------------- >> > >> > Message: 1 >> > Date: Tue, 15 May 2007 04:54:57 +0200 >> > From: Ron Korstanje >> > Subject: [rat-forum] Freezing rat sperm >> > To: >> > Message-ID: >> > Content-Type: text/plain; charset="US-ASCII" >> > >> > Dear forum, >> > >> > We would like to freeze rat sperm from two lines and send it abroad >> to have >> > it assayed on oocyte binding capability (we suspect differences >> between the >> > lines). >> > However, I have heard from various sources that frozen rat sperm is not >> > capable of binding anymore. >> > >> > Is this true, or are there protocols that might be successful? >> > >> > thanks, >> > >> > Ron >> > >> > >> > Ron Korstanje, PhD >> > >> > University Medical Center Groningen >> > Medical Biology division >> > Hanzeplein 1 >> > 9713 GZ Groningen >> > The Netherlands >> > phone: +31-50 3635777 >> > email: r.korstanje@med.umcg.nl >> > >> > >> > >> > >> > >> > ------------------------------ >> > >> > Message: 2 >> > Date: Thu, 17 May 2007 01:15:21 -0400 >> > From: dong bing >> > Subject: [rat-forum] how to acquire rat embryo blood >> > To: >> > Message-ID: >> > Content-Type: text/plain; charset="iso-8859-1" >> > >> > Hi guys, >> > >> > Good to find this forum by google hunting to ask rat-related >> questions in lab experiments. >> > >> > We designed an experiment to acquire blood from embryonic rat (20 >> gestation days). Could you please supply with methods? Thanks >> > >> > Bing >> > _________________________________________________________________ >> > Add some color. Personalize your inbox with your favorite colors. >> > >> www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0507 >> >> >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: >> http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070517/e56a14e1/attachment-0001.html >> >> > >> > ------------------------------ >> > >> > Message: 3 >> > Date: Thu, 17 May 2007 09:05:05 -0500 >> > From: Hershel Raff >> > Subject: Re: [rat-forum] how to acquire rat embryo blood >> > To: Rat Community Forum >> > Message-ID: <464C6111.6070008@mcw.edu> >> > Content-Type: text/plain; charset="us-ascii" >> > >> > Please clarify. Do you mean other than doing a cesarian section and >> > decapitating the E20 fetuses? HR >> > >> > dong bing wrote: >> > >> > > Hi guys, >> > > >> > > Good to find this forum by google hunting to ask rat-related >> > > questions in lab experiments. >> > > >> > > We designed an experiment to acquire blood from embryonic rat (20 >> > > gestation days). Could you please supply with methods? Thanks >> > > >> > > Bing >> > > >> > > >> ------------------------------------------------------------------------ >> > > Change is good. See what's different about Windows Live Hotmail. >> Check >> > > it out! >> > > < >> www.windowslive-hotmail.com/learnmore/default.html?locale=en-us&ocid=RMT_TAGLM_HMWL_reten_changegood_0507 >> >> > >> > > >> > > >> > >> >------------------------------------------------------------------------ >> > > >> > >_______________________________________________ >> > >rat-forum mailing list >> > >rat-forum@mcw.edu >> > > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum >> > > >> > > >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: >> http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070517/b9308adb/attachment-0001.html >> >> > >> > ------------------------------ >> > >> > Message: 4 >> > Date: Fri, 18 May 2007 09:43:40 +0900 >> > From: "Birger Voigt" >> > Subject: RE: [rat-forum] Freezing rat sperm >> > To: "Rat Community Forum" >> > Message-ID: >> > <4D963D0E0320AD4BA7B54D58BC9A89D442E0B3@mail.anim.med.kyoto-u.ac.jp> >> > Content-Type: text/plain; charset="us-ascii" >> > >> > Hello Ron, >> > There are several protocols for in-vitro-fertilization using frozen >> sperms. I >> > think they would not be able of fertilizing any ovum in case they >> would had >> > lost their binding capability. >> > We are currently preparing a DVD manual in English for several >> > cryopreservation methods in the rat that includes also protocols >> for sperm >> > freezing. If you are interested, please contact me directly. >> > Regards, >> > Birger Voigt >> > >> > >> > Birger Voigt, PhD >> > Institute of Laboratory Animals >> > Graduate School of Medicine >> > Kyoto University >> > Sakyo-ku >> > Kyoto, 606-8501 >> > Japan >> > Tel.: +81 75 753 9318 >> > Fax.: +81 75 753 4409 >> > e-mail: birger@anim.med.kyoto-u.ac.jp >> > HP: www.anim.med.kyoto-u.ac.jp/NBR >> >> > >> > >> > >> > -----Original Message----- >> > From: rat-forum-bounces@mcw.edu [ mailto:rat-forum-bounces@mcw.edu] >> On Behalf >> > Of Ron Korstanje >> > Sent: Dienstag, 15. Mai 2007 11:55 >> > To: rat-forum@mcw.edu >> > Subject: [rat-forum] Freezing rat sperm >> > >> > Dear forum, >> > >> > We would like to freeze rat sperm from two lines and send it abroad >> to have >> > it assayed on oocyte binding capability (we suspect differences >> between the >> > lines). >> > However, I have heard from various sources that frozen rat sperm is not >> > capable of binding anymore. >> > >> > Is this true, or are there protocols that might be successful? >> > >> > thanks, >> > >> > Ron >> > >> > >> > Ron Korstanje, PhD >> > >> > University Medical Center Groningen >> > Medical Biology division >> > Hanzeplein 1 >> > 9713 GZ Groningen >> > The Netherlands >> > phone: +31-50 3635777 >> > email: r.korstanje@med.umcg.nl >> > >> > >> > >> > _______________________________________________ >> > rat-forum mailing list >> > rat-forum@mcw.edu >> > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum >> > >> > >> > ------------------------------ >> > >> > Message: 5 >> > Date: Tue, 22 May 2007 19:08:45 -0500 >> > From: Bruce McCallum >> > Subject: Re: [rat-forum] Housekeeping genes for RT-PCR >> > To: Rat Community Forum >> > Message-ID: <9628D745-3FAF-43A7-9185-A74F00415B0C@mcw.edu> >> > Content-Type: text/plain; charset="us-ascii" >> > >> > George, >> > Is it possible to forward a digital copy of the Biotechniques >> > article? The April issue is stuck deep in the bowels of the >> > circulation department, and our library does not subscribe to the >> > digital service. >> > Thanks, >> > -bmc >> > On Apr 24, 2007, at 3:11 PM, George Cicila wrote: >> > >> > > Robert, >> > > There was a recent article in Biotechniques by Hong et al. >> > > [Biotechniques 42(4):503-512. 2007] that deals with your question. >> > > They conducted a microarray and qRT-PCR study, and recommend >> > > control genes for 11 rat tissues (unfortunately not pancreas). >> > > >> > > George Cicila >> > > >> > > >> > > On 4/24/07 3:10 PM, "Robert Wallis" wrote: >> > > >> > >> Dear rat forum subscribers >> > >> >> > >> We are trying to find a suitable housekeeping gene to normalise to >> > >> using real time pcr (at the moment we are looking in the >> > >> pancreas). We are presently having 'issues' with beta actin; >> > >> similar sized bands appear from both genomic and cDNA, even though >> > >> designed over an exon-exon boundary, with 3 different designs of >> > >> primers plus a commercially available one, (who mentioned it may >> > >> be due to an extra pseudogene, giving the excuse that the rat >> > >> sequence is not as well validated as it's mouse and human >> > >> counterparts) >> > >> >> > >> Suffice to say; has anyone had similar issues regarding >> > >> housekeeping genes in the rat, and have you any advice on which >> > >> housekeeping genes to use, and perhaps more importantly which to >> > >> avoid? >> > >> >> > >> Many Thanks >> > >> >> > >> >> > >> Robert Wallis >> > >> >> > >> Sunnybrook Research Institute >> > >> Division of Molecular and Cell Biology >> > >> 2075 Bayview Avenue; RM A3-31 >> > >> Toronto >> > >> Ontario >> > >> M4N 3M5 >> > >> CANADA >> > >> >> > >> Tel; 416 480 6100 xt 7297 (lab) xt 7293 (office) >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> _______________________________________________ >> > >> rat-forum mailing list >> > >> rat-forum@mcw.edu >> > >> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum >> > > >> > > _______________________________________________ >> > > rat-forum mailing list >> > > rat-forum@mcw.edu >> > > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum >> > >> > J. Bruce McCallum >> > Research Scientist >> > Department of Anesthesiology, M4340 >> > Medical College of Wisconsin >> > 8701 Watertown Plank Rd. >> > Milwaukee, WI 53226 >> > Phone: (414)456-5682 >> > FAX: (414)456-6507 >> > >> > >> > >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: >> http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070522/640d5248/attachment-0001.html >> >> > >> > ------------------------------ >> > >> > Message: 6 >> > Date: Thu, 31 May 2007 15:26:48 +0200 >> > From: Philip Zimmermann >> > Subject: [rat-forum] Genevestigator releases rat expression data >> > To: rat-forum@mcw.edu >> > Message-ID: <465ECD18.5080705@ethz.ch> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > Dear All, >> > >> > The Swiss Federal Institute of Technology Zurich (ETH Zurich) has >> > recently released a new version of Genevestigator, a popular >> expression >> > meta-analysis tool previously containing only mouse and arabidopsis >> > data. The new version now contains 2894 quality-controlled and curated >> > rat microarrays from 94 public experiments. Many of these experiments >> > are from toxicogenomics. >> > >> > Genevestigator was designed by biologists, developed by software >> > engineers, and is user-friendly with biologists as end-users in mind. >> > The classical tools allow users to look at how genes are expressed in >> > many different tissues, developmental stages, stimuli, drug >> treatments, >> > diseases, and genetic modifications. More recently developed advanced >> > tools additionally allow to search for biomarkers, cluster genes with >> > similar meta-profiles, and project expression data onto metabolic >> > networks (mouse and arabidopsis). >> > >> > The classical tools are freely available for academic users. Just be >> > sure you have Java 1.4.2 or higher on your computer to run the >> analysis >> > tool. Genevestigator can be found at: >> > https://www.genevestigator.ethz.ch >> >> > >> > Some screenshots are available here: >> > >> https://www.genevestigator.ethz.ch/index.php?option=com_content&task=view&id=49 >> >> >> > >> > The tools might be of interest to molecular biologists and scientists >> > working in toxicogenomics and diagnostics. >> > >> > Philip Zimmermann, ETH Zurich, Switzerland >> > >> > -- >> > ETH Zurich >> > Dr. Philip Zimmermann >> > Genevestigator / Bioinformatics >> > Universit?tsstrasse 2 >> > 8092 Zurich, Switzerland >> > >> > phz@ethz.ch >> > http://www.pb.ethz.ch >> > https://www.genevestigator.ethz.ch >> >> > +41 44 632 67 32 (phone office) >> > >> > >> > >> > ------------------------------ >> > >> > Message: 7 >> > Date: Fri, 1 Jun 2007 10:19:41 -0500 >> > From: "Shimoyama, Mary" >> > Subject: [rat-forum] RGD NEW RELEASE - New data for rat genes >> > To: >> > Message-ID: >> > <1448A38A42714048B9C53E473E13CCF0CA61D8@davis.hmgc.mcw.edu> >> > Content-Type: text/plain; charset="us-ascii" >> > >> > ANNOUNCING NEW RGD RELEASE >> > >> > RGD is happy to announce its 3rd major release of 2007. This release >> > includes the addition of Celera genome positions for genes >> > >> > >> > >> > Celera Genome Positions >> > >> > RGD now provides genomic positions for genes on the Celera Assembly >> > http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=3876 >> > >> > as well as a Celera Assembly option on the GBrowse to provide users >> with >> > a view of data elements within the context of the Celera Assembly. >> > >> > >> > >> > New Protein Links >> > >> > Weekly updates of data from the International Protein Index now provide >> > users with the most up to date links to essential protein and family >> > information and identifiers including IPI, UNIPARC, Ensembl Protein, >> > InterPro, Pfam, PRINTS, PROSITE, PANTHER, RZPD, SMART, ProDom, >> > Superfamily-SCOP, TIGRFAM, and Gene3D-Cath. >> > ( http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=621533) >> > >> > >> > >> > Disease Genes >> > >> > The Rat orthologs of 1547 genes listed at OMIM have been fully curated >> > using all rat papers published on each gene. >> > >> > >> > >> > Gene Families and Nomenclature >> > >> > The nomenclature for two major gene families, alpha tubulin and >> > prolactin related genes has been completed. Identification and >> > nomenclature assignment was coordinated with Dr. Michael Soares and the >> > Mouse Genome Database. Details were published in Soares et al, >> > Mammalian Genome 2007, Mar 18(3):154-6 >> > http://rgd.mcw.edu/tools/references/references_view.cgi?id=1624237 A >> > publication on the nomenclature resolution of the alpha tubulin family >> > will appear in Genomics soon. >> > >> > >> > >> > >> > >> > Mary Shimoyama >> > >> > Program Manager >> > >> > Rat Genome Database >> > >> > Human and Molecular Genetics Center >> > >> > Medical College of Wisconsin >> > >> > shimoyama@mcw.edu >> > >> > Tel: 414-456-7505 >> > >> > Fax: 414-456-6595 >> > >> > http://rgd.mcw.edu >> > >> > >> > >> > >> > >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: >> http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070601/ede5c42c/attachment.html >> >> > >> > ------------------------------ >> > >> > _______________________________________________ >> > rat-forum mailing list >> > rat-forum@mcw.edu >> > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum >> > >> > >> > End of rat-forum Digest, Vol 3, Issue 1 >> > *************************************** >> >> ------------------------------------------------------------------------ >> Change is good. See what's different about Windows Live Hotmail. >> Check it out! >> _______________________________________________ >> rat-forum mailing list >> rat-forum@mcw.edu >> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > >------------------------------------------------------------------------ > >_______________________________________________ >rat-forum mailing list >rat-forum@mcw.edu >http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070611/6051d288/attachment-0001.html From simont at hmgc.mcw.edu Tue Jun 12 09:04:13 2007 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Tue Jun 12 13:55:44 2007 Subject: [rat-forum] Prototype rat SNP visualization tool at RGD Message-ID: Dear List, We have been working with Norbert Hubner and the STAR consortium (http://www.snp-star.de/) to develop some visualization tools for their upcoming SNP dataset. The full dataset of approximately 20,000+ SNPs genotyped in over 300+ rat strains is anticipated to be released shortly via Ensembl, however, in the meantime we've put 100 SNPs from a preliminary version of the dataset online for people to try. The SNPs have been loaded from around the Sah gene on Chromosome 1 (ca. 178,070,000 bp) so there is data for SNPs between 174,485,928 bp and 185,692,567 bp. You can find the tool at this URL: http://snplotyper.mcw.edu This tool is open source and available via Rubyforge: http:// rubyforge.org/projects/snplotyper The SNP and strain symbols you will see on the tool are not their final versions, we are working to get official nomenclature for all the strains and SNPs for the full release. At this point we'd like people to try the tool and give us some feedback on desired features, improvements to the presentation, etc. so we can plan where to go from here and have things in place for when the full data set becomes available. We look forward to questions and comments. Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From hjpark at kitox.re.kr Wed Jun 13 03:35:54 2007 From: hjpark at kitox.re.kr (=?ks_c_5601-1987?B?udrH0cH4?=) Date: Wed Jun 13 08:16:56 2007 Subject: [rat-forum] Leydig cell isolation & purification from rat testis Message-ID: <200706130835.l5D8ZtZ10826@mail.kitox.re.kr> Dear rat forum subscribers We are trying to isolate mRNA of Leydig cell from testis of rat (after administration of reproductive toxic chemicals). There are several papers describing the methods how to isolate pure Leydig cell. However, most methods are too simple to apply to our work. Does anybody help me where I could get more detailed methods? Thank you for your helps. Hanjin Park __________________________________ Toxicogenomics Team Korea Institute of Toxicology (KIT) P.O. Box123, Yuseong, Daejeon, Republic of Korea Tel: +82-42-860-7044 / Fax: +82-42-860-7488 E-mail: hjpark@kitox.re.kr KIT Home: www.kitox. re.kr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070613/4c37d1aa/attachment.html From gbot at taconic.com Thu Jun 14 08:41:03 2007 From: gbot at taconic.com (Gerald Bothe) Date: Thu Jun 14 09:26:32 2007 Subject: [rat-forum] Prototype rat SNP visualization tool at RGD In-Reply-To: References: Message-ID: <46710D2F020000B20006AE1F@mail2.taconic.com> I have been trying several pairs of rat strains (e.g. first DA vs. F344, BN vs F344), and I always get "0 SNPs in this region" in the yellow field in the middle of the screen. Do you have a test pair/settings that work? Thanks Gerald Gerald W. Bothe, Ph. D. Senior Scientist, R&D Taconic Biotechnology 5 University Place Rensselaer, NY 12144 (518) 257 2030 ext. 12126 >>> Twigger Simon 6/12/2007 10:04:13 AM >>> Dear List, We have been working with Norbert Hubner and the STAR consortium (http://www.snp-star.de/) to develop some visualization tools for their upcoming SNP dataset. The full dataset of approximately 20,000+ SNPs genotyped in over 300+ rat strains is anticipated to be released shortly via Ensembl, however, in the meantime we've put 100 SNPs from a preliminary version of the dataset online for people to try. The SNPs have been loaded from around the Sah gene on Chromosome 1 (ca. 178,070,000 bp) so there is data for SNPs between 174,485,928 bp and 185,692,567 bp. You can find the tool at this URL: http://snplotyper.mcw.edu This tool is open source and available via Rubyforge: http:// rubyforge.org/projects/snplotyper The SNP and strain symbols you will see on the tool are not their final versions, we are working to get official nomenclature for all the strains and SNPs for the full release. At this point we'd like people to try the tool and give us some feedback on desired features, improvements to the presentation, etc. so we can plan where to go from here and have things in place for when the full data set becomes available. We look forward to questions and comments. Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw _______________________________________________ rat-forum mailing list rat-forum@mcw.edu http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum From gbot at taconic.com Thu Jun 14 08:45:27 2007 From: gbot at taconic.com (Gerald Bothe) Date: Thu Jun 14 09:27:37 2007 Subject: [rat-forum] Prototype rat SNP visualization tool at RGD In-Reply-To: References: Message-ID: <46710E37020000B20006AE23@mail2.taconic.com> ok, my start/end selection was wrong - I had input 0 bp as start which the program did not accept. Suggestion: make 0, start etc. an option for "From" and "END" an option for the "To" field, or have a checkbox "whole chromosome", or have the program automatically return all SNPs from whole chromosome if nothing is selected. Gerald Gerald W. Bothe, Ph. D. Senior Scientist, R&D Taconic Biotechnology 5 University Place Rensselaer, NY 12144 (518) 257 2030 ext. 12126 >>> Twigger Simon 6/12/2007 10:04:13 AM >>> Dear List, We have been working with Norbert Hubner and the STAR consortium (http://www.snp-star.de/) to develop some visualization tools for their upcoming SNP dataset. The full dataset of approximately 20,000+ SNPs genotyped in over 300+ rat strains is anticipated to be released shortly via Ensembl, however, in the meantime we've put 100 SNPs from a preliminary version of the dataset online for people to try. The SNPs have been loaded from around the Sah gene on Chromosome 1 (ca. 178,070,000 bp) so there is data for SNPs between 174,485,928 bp and 185,692,567 bp. You can find the tool at this URL: http://snplotyper.mcw.edu This tool is open source and available via Rubyforge: http:// rubyforge.org/projects/snplotyper The SNP and strain symbols you will see on the tool are not their final versions, we are working to get official nomenclature for all the strains and SNPs for the full release. At this point we'd like people to try the tool and give us some feedback on desired features, improvements to the presentation, etc. so we can plan where to go from here and have things in place for when the full data set becomes available. We look forward to questions and comments. Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw _______________________________________________ rat-forum mailing list rat-forum@mcw.edu http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum From simont at hmgc.mcw.edu Thu Jun 14 09:56:39 2007 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Thu Jun 14 10:00:55 2007 Subject: [rat-forum] Prototype rat SNP visualization tool at RGD In-Reply-To: <46710E37020000B20006AE23@mail2.taconic.com> References: <46710E37020000B20006AE23@mail2.taconic.com> Message-ID: Hi Gerald, I see what you mean, thats clearly a bug on our end and I'll fix that ASAP. I thought it used to take 0 but apparently not. For others trying the tool it currently expects a number greater than zero in the From/To boxes. You can use commas to make entering large numbers easier, eg. 175,000,000 will work as will 175000000. Note that we only have data for SNPs on Chromosome 1 between 174,485,928 bp and 185,692,567 bp loaded in the tool at the moment. It also expects that the position you use in the From field is less than the number you put in the To field, I can do something more friendly with this situation too (swap the numbers internally, swap them in the form and/or print something helpful in the 'Current Selections' area). When the full dataset is in place I'd hesitate to do a whole chromosome because its going to be a lot of data and take a while to come back but clearly this isn't an unreasonable thing to do. I'll try it on our development server here and see how it works, what the file size is and how long it takes to create. Maybe for really big regions like that I should give the option to change the display so you can more easily see the pattern of conservation but with less of the individual SNP details (symbol, mapping data, etc). I could shrink the height of the genotype squares for each SNP, print a simplified bp scale on the left instead of all the SNP symbols (which would be too small to read otherwise). This way you could get something for an entire chromosome on one sensibly sized image and it wouldn't take ages to come back. You could see the patterns to identify regions of interest but then you'd have to go back in and look at smaller chunks of the chromosome to get the full blown report (as it currently exists with each SNP labeled, etc) How does that sound? Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jun 14, 2007, at 8:45 AM, Gerald Bothe wrote: > ok, my start/end selection was wrong - I had input 0 bp as start > which the program did not accept. Suggestion: make 0, start etc. an > option for "From" and "END" an option for the "To" field, or have a > checkbox "whole chromosome", or have the program automatically > return all SNPs from whole chromosome if nothing is selected. > > Gerald > > > Gerald W. Bothe, Ph. D. > Senior Scientist, R&D > Taconic Biotechnology > 5 University Place > Rensselaer, NY 12144 > (518) 257 2030 ext. 12126 > > >>>> Twigger Simon 6/12/2007 10:04:13 AM >>> > Dear List, > > We have been working with Norbert Hubner and the STAR consortium > (http://www.snp-star.de/) to develop some visualization tools for > their upcoming SNP dataset. The full dataset of approximately 20,000+ > SNPs genotyped in over 300+ rat strains is anticipated to be released > shortly via Ensembl, however, in the meantime we've put 100 SNPs from > a preliminary version of the dataset online for people to try. The > SNPs have been loaded from around the Sah gene on Chromosome 1 (ca. > 178,070,000 bp) so there is data for SNPs between 174,485,928 bp and > 185,692,567 bp. > > You can find the tool at this URL: > > http://snplotyper.mcw.edu > > This tool is open source and available via Rubyforge: http:// > rubyforge.org/projects/snplotyper > > The SNP and strain symbols you will see on the tool are not their > final versions, we are working to get official nomenclature for all > the strains and SNPs for the full release. At this point we'd like > people to try the tool and give us some feedback on desired features, > improvements to the presentation, etc. so we can plan where to go > from here and have things in place for when the full data set becomes > available. > > We look forward to questions and comments. > > Simon. > > > -- > > Simon N. Twigger, Ph.D. > Assistant Professor, Department of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Road, > Milwaukee, WI, USA > tel: 414-456-8802 > fax: 414-456-6595 > AIM/iChat: simontatmcw > > > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum From gbot at taconic.com Thu Jun 14 10:25:31 2007 From: gbot at taconic.com (Gerald Bothe) Date: Thu Jun 14 10:51:23 2007 Subject: [rat-forum] Prototype rat SNP visualization tool at RGD In-Reply-To: References: <46710E37020000B20006AE23@mail2.taconic.com> Message-ID: <467125AB020000B20006AE5E@mail2.taconic.com> Hi Simon, I have displayed the markers for DA and F344/N... and have some more comments: - the browser displays SNPs that are the same for both strains. It would be good to have the option to exclude these. - for even better strain comparisons, one could have two windows for "Strains". A marker would have to be the same for all the strains marked in window 1 and different from all the strains marked in window 2. This would be an advanced feature useful in genetic monitoring/quality control of breeding colonies - the browser displays SNPs where one of the two strains has no data. One could add 0%, 10%, 20% etc. to the options in "Optional Marker Filters" - the browser displays SNPs that are het in one of the strains. How about an option to display only hets (in outbred strains) or to exclude hets? Gene frequency at heterozygous loci is interesting for studying genetic drift in outbred populations, admittedly a niche application... but excluding hets would be practical for all people looking at inbreds. All the best Gerald Gerald W. Bothe, Ph. D. Senior Scientist, R&D Taconic Biotechnology 5 University Place Rensselaer, NY 12144 (518) 257 2030 ext. 12126 >>> Twigger Simon 6/14/2007 10:56:39 AM >>> Hi Gerald, I see what you mean, thats clearly a bug on our end and I'll fix that ASAP. I thought it used to take 0 but apparently not. For others trying the tool it currently expects a number greater than zero in the From/To boxes. You can use commas to make entering large numbers easier, eg. 175,000,000 will work as will 175000000. Note that we only have data for SNPs on Chromosome 1 between 174,485,928 bp and 185,692,567 bp loaded in the tool at the moment. It also expects that the position you use in the From field is less than the number you put in the To field, I can do something more friendly with this situation too (swap the numbers internally, swap them in the form and/or print something helpful in the 'Current Selections' area). When the full dataset is in place I'd hesitate to do a whole chromosome because its going to be a lot of data and take a while to come back but clearly this isn't an unreasonable thing to do. I'll try it on our development server here and see how it works, what the file size is and how long it takes to create. Maybe for really big regions like that I should give the option to change the display so you can more easily see the pattern of conservation but with less of the individual SNP details (symbol, mapping data, etc). I could shrink the height of the genotype squares for each SNP, print a simplified bp scale on the left instead of all the SNP symbols (which would be too small to read otherwise). This way you could get something for an entire chromosome on one sensibly sized image and it wouldn't take ages to come back. You could see the patterns to identify regions of interest but then you'd have to go back in and look at smaller chunks of the chromosome to get the full blown report (as it currently exists with each SNP labeled, etc) How does that sound? Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jun 14, 2007, at 8:45 AM, Gerald Bothe wrote: > ok, my start/end selection was wrong - I had input 0 bp as start > which the program did not accept. Suggestion: make 0, start etc. an > option for "From" and "END" an option for the "To" field, or have a > checkbox "whole chromosome", or have the program automatically > return all SNPs from whole chromosome if nothing is selected. > > Gerald > > > Gerald W. Bothe, Ph. D. > Senior Scientist, R&D > Taconic Biotechnology > 5 University Place > Rensselaer, NY 12144 > (518) 257 2030 ext. 12126 > > >>>> Twigger Simon 6/12/2007 10:04:13 AM >>> > Dear List, > > We have been working with Norbert Hubner and the STAR consortium > (http://www.snp-star.de/) to develop some visualization tools for > their upcoming SNP dataset. The full dataset of approximately 20,000+ > SNPs genotyped in over 300+ rat strains is anticipated to be released > shortly via Ensembl, however, in the meantime we've put 100 SNPs from > a preliminary version of the dataset online for people to try. The > SNPs have been loaded from around the Sah gene on Chromosome 1 (ca. > 178,070,000 bp) so there is data for SNPs between 174,485,928 bp and > 185,692,567 bp. > > You can find the tool at this URL: > > http://snplotyper.mcw.edu > > This tool is open source and available via Rubyforge: http:// > rubyforge.org/projects/snplotyper > > The SNP and strain symbols you will see on the tool are not their > final versions, we are working to get official nomenclature for all > the strains and SNPs for the full release. At this point we'd like > people to try the tool and give us some feedback on desired features, > improvements to the presentation, etc. so we can plan where to go > from here and have things in place for when the full data set becomes > available. > > We look forward to questions and comments. > > Simon. > > > -- > > Simon N. Twigger, Ph.D. > Assistant Professor, Department of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Road, > Milwaukee, WI, USA > tel: 414-456-8802 > fax: 414-456-6595 > AIM/iChat: simontatmcw > > > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum _______________________________________________ rat-forum mailing list rat-forum@mcw.edu http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum From peter.a.doris at uth.tmc.edu Thu Jun 14 10:18:49 2007 From: peter.a.doris at uth.tmc.edu (Peter Doris) Date: Thu Jun 14 10:52:02 2007 Subject: [rat-forum] Prototype rat SNP visualization tool at RGD In-Reply-To: Message-ID: Dear Simon: This looks very nice. Thanks for your efforts in making this available and opening a prototype. A few questions: 1. Can you indicate whether there will be an option that would allow all SNP's for the strains searched across the region searched to be exported (eg to .xls, tabbed text etc)? 2. Are you able to enlarge upon: "anticipated to be released shortly via Ensembl" 3. Also, some genotyping tools that might be applied to extracts of this data set may use PCR in which a primer design step would be necessary. Does this tool provide any additional means to extract adjacent sequence context other than what is shown in the "Marker Table" view?? Peter -- Peter A. Doris, Ph.D. Associate Professor Center for Human Genetics Institute of Molecular Medicine University of Texas Health Science Center Suite 530F 1825 Pressler Houston, TX 77030-3725 Peter.A.Doris@uth.tmc.edu Home page: http://www.uth.tmc.edu/uth_orgs/imm/faculty/doris.htm Recent publications: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=PubMed&cmd=search& term=doris%20pa (713) 500 2414 (713) 500 2447 FAX > From: Twigger Simon > Reply-To: Rat Community Forum > Date: Tue, 12 Jun 2007 09:04:13 -0500 > To: Rat Forum Community > Subject: [rat-forum] Prototype rat SNP visualization tool at RGD > > Dear List, > > We have been working with Norbert Hubner and the STAR consortium > (http://www.snp-star.de/) to develop some visualization tools for > their upcoming SNP dataset. The full dataset of approximately 20,000+ > SNPs genotyped in over 300+ rat strains is anticipated to be released > shortly via Ensembl, however, in the meantime we've put 100 SNPs from > a preliminary version of the dataset online for people to try. The > SNPs have been loaded from around the Sah gene on Chromosome 1 (ca. > 178,070,000 bp) so there is data for SNPs between 174,485,928 bp and > 185,692,567 bp. > > You can find the tool at this URL: > > http://snplotyper.mcw.edu > > This tool is open source and available via Rubyforge: http:// > rubyforge.org/projects/snplotyper > > The SNP and strain symbols you will see on the tool are not their > final versions, we are working to get official nomenclature for all > the strains and SNPs for the full release. At this point we'd like > people to try the tool and give us some feedback on desired features, > improvements to the presentation, etc. so we can plan where to go > from here and have things in place for when the full data set becomes > available. > > We look forward to questions and comments. > > Simon. > > > -- > > Simon N. Twigger, Ph.D. > Assistant Professor, Department of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Road, > Milwaukee, WI, USA > tel: 414-456-8802 > fax: 414-456-6595 > AIM/iChat: simontatmcw > > > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum From akwitek at mcw.edu Thu Jun 14 11:12:19 2007 From: akwitek at mcw.edu (Kwitek, Anne) Date: Thu Jun 14 11:25:22 2007 Subject: [rat-forum] CSHL Meeting Announcement: Rat Genomics and Models 2007 In-Reply-To: Message-ID: <1448A38A42714048B9C53E473E13CCF0011298E6@davis.hmgc.mcw.edu> The organizers of the 2007 Cold Spring Harbor Rat Genomics and Models meeting would like to announce the final program of the meeting, to be held December 6-9, 2007. Please go to the CSHL website for information - http://meetings.cshl.edu/meetings/rodent07.shtml This promises to be an excellent meeting. The CSHL venue offers unique opportunities for close interaction with leaders in the field and generation of stimulating scientific discussion. Hope to see you there! Anne Kwitek on behalf of the organizers Tim Aitman Norbert H?bner Anne Kwitek Jim Schull From simont at hmgc.mcw.edu Thu Jun 14 14:59:28 2007 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Mon Jun 18 09:09:10 2007 Subject: [rat-forum] Prototype rat SNP visualization tool at RGD In-Reply-To: <467125AB020000B20006AE5E@mail2.taconic.com> References: <46710E37020000B20006AE23@mail2.taconic.com> <467125AB020000B20006AE5E@mail2.taconic.com> Message-ID: <5F62CFE6-9FB4-45F0-97D4-FDDC903452D9@hmgc.mcw.edu> Hi Gerald, Great points, comments below: On Jun 14, 2007, at 10:25 AM, Gerald Bothe wrote: > Hi Simon, > > I have displayed the markers for DA and F344/N... and have some > more comments: > > - the browser displays SNPs that are the same for both strains. It > would be good to have the option to exclude these. > > - for even better strain comparisons, one could have two windows > for "Strains". A marker would have to be the same for all the > strains marked in window 1 and different from all the strains > marked in window 2. This would be an advanced feature useful in > genetic monitoring/quality control of breeding colonies I think having these two groups is the correct route to take, the decision is then how to deal with missing data. Lets say you have 3 strains in group A (window 1 as you describe above) and 4 strains in Group B (window 2) and you want to find SNPs that are polymorphic between the two groups. 1) Do you exclude SNPs that do not have genotypes of each of the 7 strains? This would be very conservative but presumably give you a more confident set of SNPs. 2) Do you keep SNPs with less than a full set of genotypes (but with at least some sensible number of genotypes in each of the two groups: 2 out of 3 from group 1; 3 out of 4 in group 2?) and determine polymorphism based on the available genotypes? You would have more SNPs to pick from but there is the chance that if you knew this missing genotype data it would show that the marker was not actually polymorphic? These are actually different flavors of the same algorithm so we could have a percentage that you could set that determines the threshold of missing genotype data that would cause that SNP to be dropped from the analysis. This could be the existing % that can be set to exclude SNPs with missing data (that you mention below), but I think it would need to be applied separately to the different groups if you were using that feature, rather than across the board with all of the strains you've selected as it currently is now. In the example above you could set it to 66% so the SNP would have to have genotype data for 2 out of 3 strains in group 1 (2/3 = 66.6%, which is >= 66%) and 3 out of 4 in group 2 (3/4 = 75% which is >= 66%) in order to be considered further. If it passed this test, you would then look to see it was polymorphic with the genotype data available. If you wanted to exclude markers with any missing data (situation 1 above) you could set it to 100% and then there would need to be genotype data for all the strains and it would have to be polymorphic between the groups in order for the SNP to pass. Does this seem reasonable? > > - the browser displays SNPs where one of the two strains has no > data. One could add 0%, 10%, 20% etc. to the options in "Optional > Marker Filters" I'll add these today. > > - the browser displays SNPs that are het in one of the strains. How > about an option to display only hets (in outbred strains) or to > exclude hets? Gene frequency at heterozygous loci is interesting > for studying genetic drift in outbred populations, admittedly a > niche application... but excluding hets would be practical for all > people looking at inbreds. This shouldn't be hard to add either. > > All the best > > Gerald Thanks for the comments! Simon. > > > Gerald W. Bothe, Ph. D. > Senior Scientist, R&D > Taconic Biotechnology > 5 University Place > Rensselaer, NY 12144 > (518) 257 2030 ext. 12126 > > >>>> Twigger Simon 6/14/2007 10:56:39 AM >>> > Hi Gerald, > > I see what you mean, thats clearly a bug on our end and I'll fix that > ASAP. I thought it used to take 0 but apparently not. > > For others trying the tool it currently expects a number greater than > zero in the From/To boxes. You can use commas to make entering large > numbers easier, eg. 175,000,000 will work as will 175000000. Note > that we only have data for SNPs on Chromosome 1 between 174,485,928 > bp and 185,692,567 bp loaded in the tool at the moment. > > It also expects that the position you use in the From field is less > than the number you put in the To field, I can do something more > friendly with this situation too (swap the numbers internally, swap > them in the form and/or print something helpful in the 'Current > Selections' area). > > When the full dataset is in place I'd hesitate to do a whole > chromosome because its going to be a lot of data and take a while to > come back but clearly this isn't an unreasonable thing to do. I'll > try it on our development server here and see how it works, what the > file size is and how long it takes to create. > > Maybe for really big regions like that I should give the option to > change the display so you can more easily see the pattern of > conservation but with less of the individual SNP details (symbol, > mapping data, etc). I could shrink the height of the genotype squares > for each SNP, print a simplified bp scale on the left instead of all > the SNP symbols (which would be too small to read otherwise). This > way you could get something for an entire chromosome on one sensibly > sized image and it wouldn't take ages to come back. You could see the > patterns to identify regions of interest but then you'd have to go > back in and look at smaller chunks of the chromosome to get the full > blown report (as it currently exists with each SNP labeled, etc) How > does that sound? > > Simon. > > -- > > Simon N. Twigger, Ph.D. > Assistant Professor, Department of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Road, > Milwaukee, WI, USA > tel: 414-456-8802 > fax: 414-456-6595 > AIM/iChat: simontatmcw > > > On Jun 14, 2007, at 8:45 AM, Gerald Bothe wrote: > >> ok, my start/end selection was wrong - I had input 0 bp as start >> which the program did not accept. Suggestion: make 0, start etc. an >> option for "From" and "END" an option for the "To" field, or have a >> checkbox "whole chromosome", or have the program automatically >> return all SNPs from whole chromosome if nothing is selected. >> >> Gerald >> >> >> Gerald W. Bothe, Ph. D. >> Senior Scientist, R&D >> Taconic Biotechnology >> 5 University Place >> Rensselaer, NY 12144 >> (518) 257 2030 ext. 12126 >> >> >>>>> Twigger Simon 6/12/2007 10:04:13 AM >>> >> Dear List, >> >> We have been working with Norbert Hubner and the STAR consortium >> (http://www.snp-star.de/) to develop some visualization tools for >> their upcoming SNP dataset. The full dataset of approximately 20,000+ >> SNPs genotyped in over 300+ rat strains is anticipated to be released >> shortly via Ensembl, however, in the meantime we've put 100 SNPs from >> a preliminary version of the dataset online for people to try. The >> SNPs have been loaded from around the Sah gene on Chromosome 1 (ca. >> 178,070,000 bp) so there is data for SNPs between 174,485,928 bp and >> 185,692,567 bp. >> >> You can find the tool at this URL: >> >> http://snplotyper.mcw.edu >> >> This tool is open source and available via Rubyforge: http:// >> rubyforge.org/projects/snplotyper >> >> The SNP and strain symbols you will see on the tool are not their >> final versions, we are working to get official nomenclature for all >> the strains and SNPs for the full release. At this point we'd like >> people to try the tool and give us some feedback on desired features, >> improvements to the presentation, etc. so we can plan where to go >> from here and have things in place for when the full data set becomes >> available. >> >> We look forward to questions and comments. >> >> Simon. >> >> >> -- >> >> Simon N. Twigger, Ph.D. >> Assistant Professor, Department of Physiology >> Medical College of Wisconsin >> 8701 Watertown Plank Road, >> Milwaukee, WI, USA >> tel: 414-456-8802 >> fax: 414-456-6595 >> AIM/iChat: simontatmcw >> >> >> _______________________________________________ >> rat-forum mailing list >> rat-forum@mcw.edu >> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum >> >> _______________________________________________ >> rat-forum mailing list >> rat-forum@mcw.edu >> http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > _______________________________________________ > rat-forum mailing list > rat-forum@mcw.edu > http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum From deepakshrma at rediffmail.com Sun Jun 17 05:27:00 2007 From: deepakshrma at rediffmail.com (Dr. Deepak Sharma) Date: Mon Jun 18 09:44:53 2007 Subject: [rat-forum] Freezing rat sperm Message-ID: <1179500897.S.4826.13039.Z.webmail15.rediffmail.com.old.forward.1182076019.21974@webmail.rediffmail.com> Dear Birger, I am working on rat superovulation and embryo freezing. can you help me to standardize the same and forward the DVD. regardsDeepakOn Fri, 18 May 2007 09:43:40 +0900 Rat Community Forum wroteHello Ron,There are several protocols for in-vitro-fertilization using frozen sperms. Ithink they would not be able of fertilizing any ovum in case they would hadlost their binding capability.We are currently preparing a DVD manual in English for severalcryopreservation methods in the rat that includes also protocols for spermfreezing. If you are interested, please contact me directly.Regards,Birger VoigtBirger Voigt, PhDInstitute of Laboratory AnimalsGraduate School of MedicineKyoto UniversitySakyo-kuKyoto, 606-8501JapanTel.: +81 75 753 9318Fax.: +81 75 753 4409e-mail: birger@anim.med.kyoto-u.ac.jpHP: www.anim.med.kyoto-u.ac.jp/NBR -----Original Message-----From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On BehalfOf Ron KorstanjeSent: Dienst! ag, 15. Mai 2007 11:55To: rat-forum@mcw.eduSubject: [rat-forum] Freezing rat spermDear forum,We would like to freeze rat sperm from two lines and send it abroad to haveit assayed on oocyte binding capability (we suspect differences between thelines).However, I have heard from various sources that frozen rat sperm is notcapable of binding anymore.Is this true, or are there protocols that might be successful?thanks,RonRon Korstanje, PhD University Medical Center GroningenMedical Biology divisionHanzeplein 1 9713 GZ Groningen The Netherlands phone: +31-50 3635777email: r.korstanje@med.umcg.nl_______________________________________________rat-forum mailing listrat-forum@mcw.eduhttp://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum_______________________________________________rat-forum mailing listrat-forum@mcw.eduhttp://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum Senior Research Scientist DSE (Animal House) , Ranbaxy Research Laboratories (UNIT -II) Plot No. 20 Sector - 18, INDIA Ph. office 2342001-10(Ext- 4879), 0124-5194879 Mob. 9818635736 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070617/6289b9ba/attachment.html From tsaunder at umich.edu Mon Jun 18 09:51:03 2007 From: tsaunder at umich.edu (Thom Saunders) Date: Mon Jun 18 10:41:56 2007 Subject: [rat-forum] Re: DVD Cryo Manual In-Reply-To: <1179500897.S.4826.13039.Z.webmail15.rediffmail.com.old.forward.1182076019.21974@webmail.rediffmail.com> References: <1179500897.S.4826.13039.Z.webmail15.rediffmail.com.old.forward. 1182076019.21974@webmail.rediffmail.com> Message-ID: <8F6AAFF1546845F5323D7ACA@[172.20.104.207]> Hi Birger, Thank you for your generous offer to share your protocols on the DVD you are preparing. I you are able to send me a copy of the DVD, I would be happy to pay for the shipping costs. Sincerely yours, Thom Thom Saunders, Ph.D. Research Assistant Professor University of Michigan Transgenic Animal Model Core Room 2570B, MSRB II 1150 W. Med. Center Drive Ann Arbor, MI 48109-0674 TEL: 734-647-2910 FAX: 734-936-2622 email: tsaunder@umich.edu URL: http://www.med.umich.edu/tamc/ http://www.transtechsociety.org/ --On Sunday, June 17, 2007 10:27 AM +0000 "Dr. Deepak Sharma" wrote: > Hello Ron, > There are several protocols for in-vitro-fertilization using frozen > sperms. I > think they would not be able of fertilizing any ovum in case they would > had > lost their binding capability. > We are currently preparing a DVD manual in English for several > cryopreservation methods in the rat that includes also protocols for sperm > freezing. If you are interested, please contact me directly. > Regards, > Birger Voigt > > > Birger Voigt, PhD > Institute of Laboratory Animals > Graduate School of Medicine > Kyoto University > Sakyo-ku > Kyoto, 606-8501 > Japan > Tel.: +81 75 753 9318 > Fax.: +81 75 753 4409 > e-mail: birger@anim.med.kyoto-u.ac.jp > HP: www.anim.med.kyoto-u.ac.jp/NBR From dorsch.martina at mh-hannover.de Tue Jun 19 01:12:38 2007 From: dorsch.martina at mh-hannover.de (Martina Dorsch) Date: Tue Jun 19 08:08:18 2007 Subject: [rat-forum] Freezing rat sperm Message-ID: Dear Dr. Sharma, you will find a prorocol for rat superovulation in MM Dorsch and HJ Hedrich (1998) J. exp. Anim. Sci. 39:99-108 and a protocol for rat embryo freezing in: Hedrich H.J. Genetic Monitoring of Inbred Strains of Rats. 1 ed., Stuttgart, New York Gustav Fischer Verlag; 1990, pp274 Maybe this can help you Martina Dorsch Dr. Martina Dorsch Central Laboratory Animal Facility Hannover-Medical School Carl-Neuberg-Str. 1 30625 Hannover, Germany Tel: ++49 (0)511 532 3864 Fax: ++49 (0)511 532 3710 or: Mr. Wallbrecht jr. e-mail: abrechnung.ZTL@mh-hannover.de or: Ms. Hanaa Bagh e-mail: bagh.hanaa@mh-hannover.de phone: ++49 (0)511 532 3708 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 753 bytes Desc: not available Url : http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070619/e9e9813b/attachment.bin From dongbing75 at hotmail.com Sat Jun 23 21:01:52 2007 From: dongbing75 at hotmail.com (dong bing) Date: Mon Jun 25 09:35:49 2007 Subject: [rat-forum] sex differentiation on neonatal rats? Message-ID: Dear List, Could you please give me a clue on how to differentiate the sex of neonatal rats? Bing ************************************************ Bing Dong dongbing75@hotmail.com _________________________________________________________________ Hotmail to go? Get your Hotmail, news, sports and much more! Check out the New MSN Mobile! http://mobile.msn.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070623/c5aa39ba/attachment.html From hraff at mcw.edu Mon Jun 25 09:41:16 2007 From: hraff at mcw.edu (Hershel Raff) Date: Mon Jun 25 09:46:40 2007 Subject: [rat-forum] sex differentiation on neonatal rats? In-Reply-To: References: Message-ID: <467FD40C.702@mcw.edu> It's done by anogenital distance. I can be challenging in newborns. I strongly suggest you get your animal care people to show you. HR dong bing wrote: > Dear List, > > Could you please give me a clue on how to differentiate the sex > of neonatal rats? > > Bing > > > ************************************************ > Bing Dong dongbing75@hotmail.com > > > ------------------------------------------------------------------------ > Hotmail to go? Get your Hotmail, news, sports and much more! Check out > the New MSN Mobile > >------------------------------------------------------------------------ > >_______________________________________________ >rat-forum mailing list >rat-forum@mcw.edu >http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070625/4dcb708c/attachment.html From mbradbury at lecom.edu Mon Jun 25 09:40:58 2007 From: mbradbury at lecom.edu (Michael Bradbury) Date: Mon Jun 25 09:47:09 2007 Subject: [rat-forum] sex differentiation on neonatal rats? References: Message-ID: Bing, One way is to examine the ano-genital distance, which will be longer in males than in females. --------------------------------------------- Michael W. Bradbury, Ph.D. Assistant Professor of Biochemistry and Medical Genetics Lake Erie College of Osteopathic Medicine 1858 W Grandview Blvd Erie, PA 16509 (814) 866-8449 mbradbury@lecom.edu --------------------------------------------- _____ From: rat-forum-bounces@mcw.edu [mailto:rat-forum-bounces@mcw.edu] On Behalf Of dong bing Sent: Saturday, June 23, 2007 10:02 PM To: rat-forum@mcw.edu Subject: [rat-forum] sex differentiation on neonatal rats? Dear List, Could you please give me a clue on how to differentiate the sex of neonatal rats? Bing ************************************************ Bing Dong dongbing75@hotmail.com _____ Hotmail to go? Get your Hotmail, news, sports and much more! Check out the New MSN Mobile -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070625/5db7e5a8/attachment.html From e-redei at northwestern.edu Mon Jun 25 10:12:43 2007 From: e-redei at northwestern.edu (Eva E. Redei) Date: Mon Jun 25 10:16:46 2007 Subject: [rat-forum] sex differentiation on neonatal rats? In-Reply-To: <467FD40C.702@mcw.edu> References: <467FD40C.702@mcw.edu> Message-ID: <7.0.1.0.2.20070625101121.0378e070@northwestern.edu> If you have a large litter and examine their anogenital distance you can distinguish males and females fast by comparing them. At 09:41 AM 6/25/2007, Hershel Raff wrote: >It's done by anogenital distance. I can be challenging in >newborns. I strongly suggest you get your animal care people to show you. HR > >dong bing wrote: >>Dear List, >> >> Could you please give me a clue on how to differentiate the >> sex of neonatal rats? >> >>Bing >> >> >>************************************************ >>Bing Dong dongbing75@hotmail.com >> >> >> >>---------- >>Hotmail to go? Get your Hotmail, news, sports and much more! >>Check out the New MSN Mobile >> >> >> >>_______________________________________________ >>rat-forum mailing list >>rat-forum@mcw.edu >>http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum >> >_______________________________________________ >rat-forum mailing list >rat-forum@mcw.edu >http://gray.hmgc.mcw.edu/mailman/listinfo/rat-forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://gray.hmgc.mcw.edu/pipermail/rat-forum/attachments/20070625/a807041a/attachment.html