Hello again, Marg, I think I can explain what's going on. We have a series of "assemblies" of the human genome with sequential numbering: e.g. hg18, hg19 (with the hg19 assembly being the most recent). These assemblies correspond with the data found at NCBI in the following way:
hg19: Feb. 2009 (GRCh37/hg19) produced by the Genome Reference Consortium. hg18: Mar. 2006 (NCBI36/hg18) produced by the International Human Genome Sequencing Consortium. When you gathered your data on 6/2/10, you were using the hg19 assembly where RP11-707O3 is found here: Chromosome: chr9 Start: 139250847 End: 139453805 When you gathered your data on 6/3/10, you were using the hg18 assembly where RP11-707O3 is found here: Chromosome: chr9 Start: 138370668 End: 138573626 You will need to choose one assembly (either hg18 or hg19) and stick with it. To help you determine which assembly to use, you can read about them from their gateway pages: http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19 http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg18 In the future, please direct your questions to the entire genome mailing list at [email protected] -- our moderated forum for user questions and discussion. You will likely get a quicker response to your question. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu > Dear Vanessa > Here is an example of what I have seen this week... > RP11-707O3 (NOTCH1) start 139250847 end 139453805 6/2/10 > 138370668 > 138573626 6/3/10 > Based on these numbers, the bp location shifted 880179. > Please feel free to call 303-724-3148 > Thanks > > Margaret C Skokan, PRA > Dr. Marileila Garcia's Laboratory > Department of Medicine/Cancer Center > University of Colorado Health Sciences Center > Phone: (303) 724-3148 > Fax: (303) 724-3889 > Mailing Address: Campus Box 8117 > PO Box 6511 > Aurora, CO 80045 > Street Address: RC-1 South Building, Room L18-8401 > 12801 East 17th Avenue > Aurora, CO 80045 > ________________________________________ > From: Vanessa Kirkup Swing [[email protected]] > Sent: Thursday, June 03, 2010 5:06 PM > To: Skokan, Margaret C > Cc: [email protected] > Subject: Re: [Genome] data shift? > > Hi Marg, > > Assemblies, such as hg18 vs. hg19, can have differences like the ones > you have described. Is it possible that you developed your primers on a > different assembly than you viewed the next day? If this isn't the case, > please contact the mailing list again. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Margaret C Skokan" <[email protected]> > To: [email protected] > Sent: Thursday, June 3, 2010 2:34:08 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] data shift? > > To whom it may concern > > It looks as though there has been a data shift of about 200kb overnight. Is > there something wrong with the browser? I selected eight sets of clones and > developed primers yesterday and when I returned to review everything today I > noticed a dramatic difference in the start and end points of my clones. > > Thanks > Marg > > Margaret C Skokan, PRA > Dr. Marileila Garcia's Laboratory > Department of Medicine/Cancer Center > University of Colorado Health Sciences Center > Phone: (303) 724-3148 > Fax: (303) 724-3889 > Mailing Address: Campus Box 8117 > PO Box 6511 > Aurora, CO 80045 > Street Address: RC-1 South Building, Room L18-8401 > 12801 East 17th Avenue > Aurora, CO 80045 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
