What's New at BayGenomics

November 8, 2005
Previously characterized ES cell line information now available. At the request of the NHLBI Programs for Genomic Applications External Scientific Panel, we now provide a list of the ES clones previously obtained and validated, including indication (when known) of whether a particular knock-out has been propagated through the germ line. In is anticipated that this data will help researchers in the selection and ordering of ES cells. The information is available from here.

October 12, 2005
Trace file comparison capability. Available under the "Other Data" tab on the Data Access page, you can now compare any trace file to that of an existing Baygenomics cell line. The submitted trace file will undergo the same 5'RACE automated protocol applied to all Baygenomics trace files. The resulting sequence tag will appear below, along with the sequence for the existing Baygenomics cell line and a multiple alignment of the two.

August 15, 2005
International Gene Trap Consortium (IGTC) web site released. The IGTC web site, hosted by BayGenomics, provides a centralized portal to all publicly available mouse gene trap cell lines, from BayGenomics and from other member organizations around the world. Information on gene trap technology and tutorials on browsing and searching the data are also included. See www.genetrap.org for details.

April 14-15, 2005
First International Gene Trap Consortium (IGTC) Informatics Workshop. Participants from six gene trapping centers in the US, Canada, Europe, and Japan participated in a workshop, hosted by BayGenomics and held in San Francisco on April 14-15, to discuss common goals and improved methods for identifying and annotating gene trap data and disseminating this data via a common web site for use by the greater scientific community. The workshop included presentations from each of the six participating gene trapping centers and from other genome informatics resource centers including Ensembl, UC Santa Cruz, NCBI, and Jackson Labs. Different approaches to gene trap annotation and localization were discussed, and a prototype annotation pipeline and associated web site under development by the Baygenomics Informatics Group was demonstrated. There was general agreement among the participants that a new IGTC web site should be created that incorporates all publically available gene trap data, and that such a web site would likely prove to be a key informatics resource for the gene trapping community.

March 11, 2005
Gene and sequence tag alignment images now available on gene annotation pages. The alignments graphically depict where sequence tags align on a particular gene. An example of an alignment image on a gene annotation page is available here. For a description of the colors and symbols used in the alignment image, click on the legend button located near the upper right side of the alignment image.

October 21, 2004
Custom annotation track on the UCSC browser. A custom annotation track for BayGenomics is now available on the UCSC browser. It can be found on the "Custom Links" page. The BayGenomics entry is located under the heading "Mouse Genome".

June 7, 2004
Instructions for viewing genetags on the Ensembl and UCSC genome browsers available. Specific directions for viewing BayGenomics genetags on the Ensembl and UCSC genome browsers are available here. They can also be accessed under the "Other Data" tab on the Data Access page.

May 21, 2004
Cell Line History now available. It is now possible to view the history of any cell line by clicking on the history link located next to the "Last Updated" category on the annotation page. The history will display a timeline of changes (if any) that have been made to the cell line. In addition, you can search for the history of any cell line by clicking "Search Cell Line History" under the "Other Data" tab found on the Data Access page.

May 18, 2004
Link to dbGSS added to annotation pages. We now provide the NCBI Genome Survey Sequences Database (dbGSS) accession number for all cell lines. The dbGSS accession number is linked to the NCBI annotation page for that particular cell line.

May 13, 2004
Vector designation incorrect for 13 cell lines. We recently discovered that the vector designation was listed incorrectly for 13 trap lines. For RRF, RRG, RRH, RRI, RRJ, RRM, RRN, RRP, RRR, RRS, RRT, and RRU, the correction was made by changing the vector designation from pGT2lxf to pGT0lxf; and for STA, the correction was made by changing the vector designation from pGT0TMpfs to pGT2TMpfs. The only difference between the two vectors is one frameshift. There are no consequences for researchers using these cell lines. Please contact us with any questions or concerns.

March 10, 2004
Cell line sequence errors detected in database. We have discovered that sequences for 436 cell lines in our database were not completely stripped of vector sequence before the sequences were posted on the website. We have corrected our database with revised sequences. A list of all affected cell lines is given here. The correction has resulted in changed identifications for only 28 annotated cell lines; the rest have no changes in identification. For every cell line revised, a comment noting the change appears at the bottom of the annotation page of the affected cell line.

July 3, 2003
LocusLink Identifiers added to database. We have incorporated LocusLink Identifiers into the BayGenomics database. You can now search for cell lines that match particular LocusID numbers on our search page, you can fetch LocusIDs as part of our Advanced Data Download feature, and LocusIDs are provided on cell line annotation pages when available.

June 12, 2003
Link to "best mouse EST" added to annotation pages. We now provide a link to NCBI's dbEST database for cell lines which can be identified with specific EST sequences. In addition to the link to NCBI, we report the quality of the match between the cell line sequence and the mouse EST sequence. A link labeled "BLAST" is also available that will automatically run a BLAST search at NCBI against all GenBank mouse EST entries so that users can obtain a list of all EST matches against a particular cell line sequence, and not just the best single match which we report.

May 22, 2003
BayGenomics cell line sequences now available in dbGSS. BayGenomics cell line sequences are now available as part of the NCBI's Genome Survey Sequences Database (dbGSS). Search for the keyword "baygenomics" at the dbGSS web site for a list of all BayGenomics sequences. New sequences are automatically posted to the dbGSS web site at the beginning of each month for sequences which are older than 30 days.

April 24, 2003
More flexible BLAST searching. Now when you BLAST the BayGenomics' database, you can search against either cell line sequences or the sequences of genes we've associated with these cell lines.

April 1, 2003
Clone IDs now available. Clone ID numbers corresponding to genes that have been trapped by BayGenomics are now available. These can be used to order full-length clones from Invitrogen. GenBank accession numbers of trapped genes and their associated clone IDs may be downloaded using our Advanced Download page. The protocol we use for associating clone IDs with genes is described here.

March 27, 2003
Cell line sequence errors detected in database. We have recently discovered that the sequences for 262 cell lines in our database were contaminated with genetrap vector sequences. Essentially we failed to strip out the vector sequence before posting the cell line sequence. We subsequently went on to associate a small number of these cell lines with Genbank entries primarily based on the vector sequence. The list of affected cell lines is given here. We will soon be correcting our database with the revised sequences. A comment at the bottom of the annotation page of each affected cell line will note any changes.

February 26, 2003
Complete DNA microarray data now available. The original complete datasets from our various Expression Profiling and Analysis Studies can now be viewed on the BayGenomics' NOMAD server. Just select "Experiments" from the options listed on NOMAD's main page.

February 24, 2003
In-situ images now linked with identified genes. Many images obtained from our in-situ hybridization studies are now directly linked to genes identified with BayGenomics cell lines. You can browse the list of genes with associated images and a description of the protocol we use to link images to genes is available.

January 20, 2003
New look for cell line annotation pages. We've made several improvements to our cell line annotation pages. For each cell line, there are now links to the UCSC Mouse Genome Browser and the Ensembl Mouse Genome Server. For each identified cell line we provide a link to the relevant GenBank entry, as well as the links to LocusLink and MGI when they exist. For cell line entries that match multiple genes using our automated annotation protocol, we provide the match critera that was used for each identification. Lastly, each annotation page has a link to the Mutant Mouse Regional Resource Centers website so that ES cell lines can be requested.

December 4, 2002
Ensembl's Mouse Genome Server now includes BayGenomics gene-trap data. BayGenomics gene-trap data has been added to Ensembl's Mouse Genome Server. Display of gene-trap data is enabled by selecting "BayGen. GeneTrap" from the drop-down menu of "DAS Sources" in the ContigView display.

November 27, 2002
BayGenomics sequence tags can now be viewed using UCSC's Genome Browser. It's now possible to view all BayGenomics sequence tags using UCSC's Mouse Genome Browser. BayGenomics creates a BLAT annotation track of BayGenomics sequence tags each time our database is updated. This sequence tag track is then displayed along with other tracks, like RefSeq genes and mouse ESTs, when browsing the physical mouse genome. This default link to the UCSC Genome Browser displays the first 10M bases of chromosome 1, but it is easy to navigate to other regions and/or other chromosomes. A convenient link to the Genome Browser can be found our on new Access Associated Data page.

November 16, 2002
Auto-identification protocol has been enhanced. Several changes have been made to our automated cell line identification protocol. These include an additional criterion used for matching tag sequences to potential genes, the addition of a new category, "Multiple Mouse IDs," and the use of UCSC's BLAT server to resolve multiple IDs to single genes when possible. See the description of our Automated Annotation Protocol for additional details.

November 5, 2002
Short sequence tags only available through Advanced Download option. Sequence tags less than 40 bp in length are now only accessible through our Advanced Download option. Short sequences are no longer stored in our BLASTable database, nor do they appear on our browse, search, or simple download data access pages, and we no longer attempt to associate genes with short sequences. This change was implemented because the marginal quality of short sequences could not reliably be used for identification purposes.

October 29, 2002
Gene trap vector sequences now available. The vector sequence used for each gene trap is now available in FASTA format by following a hyperlink on each cell line page. This is useful, for example, when designing primers for genotyping experiments.

September 14, 2002
Mutant Mouse Regional Resource Center now distributing BayGenomics ES cell lines and mutant mice. Through an exclusive agreement with BayGenomics, the NIH/NCRR-sponsored Mutant Mouse Regional Resource Center (MMRRC) is now distributing cell lines and deriving embryos and/or live mice from our cell lines. Further assistance, including genetic screening, multi-tier phenotyping, barrier housing, and colony management services, are also available from the MMRRC. To request BayGenomics ES cell lines, please contact MMRRC at UC Davis.

May 30, 2002
DNA expression microarray data now available. As part of the goals of BayGenomics project components 4 and 6, the Gladstone Genomics Core is now producing DNA microarrays containing 70-mer oligonucleotides. Currently available microarray project descriptions and associated data include:

May 6, 2002
New sequence tag classification categories. The categories that can be used when browsing or searching the BayGenomics database have been changed. The three categories are now Putative Mouse ID, Nearest Homolog, and Unidentified.

Putative Mouse ID sequences are those sequences that when compared to NCBI's non-redundant sequence database are at least 95% identical over a contiguous sequence of at least 90% of the cell line tag sequence, with allowed gaps of no more than two bases in length. This stringent criteria ensures that sequences in this category have a very high likelyhood of corresponding to the identified gene. (See our Automated Annotation Protocol for additional details.)

Nearest Homologs (any species) are those sequences that meet the much more relaxed criteria of at least 40% base identity over a contiguous sequence covering at least 80% of the cell line tag sequence. This category represents our current best attempt at identifying the nearest homolog to the sequence in question using our automated protocol. Investigators are advised to use caution when interpreting the genes identified in this category, and should inspect the detailed data presented to ensure it is appropriate for any particular use.

Unidentified sequences are those sequences that meet none of the above criteria.

Cell line entries in either the putative mouse ID or nearest homolog categories now include the sequence match criteria used to establish the particular classification; e.g. "100.0% identity over 99.8% length." Please note that we periodically run all of our sequence tag data through our auto-identification protocol, in order to match existing sequence tags with newly annotated genes. Lastly, we occasionally make refinements to our auto-identification protocol that may cause particular sequence tags to get moved from one category to another even though the underlying experimental data has not changed.

April 18, 2002
New database features. When browsing or searching the BayGenomics database, it is now possible to specify how you want your results sorted, for example by gene name, JAX symbol, or cell line name. Also, gene annotation information has been incorporated into the database (e.g. chromosome number and centimorgan position) and can be accessed through the "gene name" link on either the browse or search results pages. Lastly, IMAGE and Riken clone identifiers (CloneIDs) have been added to our database and can currently be accessed as part of our Enhanced Data Download facility. CloneIDs will soon become part of browse and search results pages too.

April 12, 2002
Enhanced data download capabilities. It is now possible to download selected fields directly from our database into a tab-delimited text file suitable for importing into applications such as Excel. All items in our database are available for download, grouped by category. You may select any number of items using a check-box type interface, and you can optionally restrict your download based on the date items were entered or updated in the database. For more information, see Enhanced Data Download.

March 4, 2002
Enhanced database browse/search capabilities. It is now possible to browse and search our Sequence Tags Database for either new or updated entries posted since a particular date. We also now track database statistics, including counts of both posted cell lines and identified genes, thereby providing a metric of our progress. And we track web site statistics as an indicator of the amount of usage our site gets.

January 15, 2002
In-situ images now available. In-situ hybridization studies as described in the component 3 overview have produced a variety of images from mouse embryos. Any gene-trapped cell lines that have associated in-situ images now have a link to the image data. You can browse the list of available images via this link.

January 7, 2002
Switch to JAX gene names. Gene names in our database are listed using the Jackson Laboratory's mouse gene name when available, otherwise the gene name from GenBank is displayed.

October 4, 2001
New web site goes live. After many weeks of work, the BayGenomics web site now has a completely new look and feel. Content has been expanded in several areas, especially those related to our bioinformatics workshops, including access to our on-line workshop tutorial. Our database search capabilities have also been enhanced. A site map is now available that has links to all content on the BayGenomics website. And a list of related links provides pointers to other related web sites.

 

Copyright © 2002 Regents of the University of California. All rights reserved.