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The TIGR Arabidopsis thaliana Database
Listed below is a collection of information on Arabidopsis genome research at TIGR.
Please follow the links to get more detailed information for each project.
Arabidopsis thaliana Annotation Database
TIGR has now finished the complete re-annotation of the Arabidopsis genome to a uniform high standard. Responsibility for maintaining the annotation currently rests with TAIR. TIGR will continue to maintain its annotation database and associated tools
and metadata.
Arabidopsis 2010 Projects
Determining
Genome-wide Transcription Networks of TGA Factors
In collaboration with Dr. Jonathan Arias (UMBC), we are using a combination
of chromatin immunoprecipitation and promoter microarrays (ChIP-chip), expression
profiling, reporter gene localization and mutant analysis to define the
transcriptional network of the TGA family of transcription factors in response
to salicylic acid.
Large Scale Analysis of Novel Arabidopsis Genes
Predicted by Comparative Genomics
The goal of this project is to generate full-length sequences for hypothetical
genes (predictions lacking database support, having very low expression
levels) and for genes that are conserved between Brassica and Arabidopsis
but not well-predicted by current algorithms. Full-length cDNAs in a Gateway®
entry vector will be made available through ABRC.
Completing the Expression
Catalog of the Arabidopsis Transcriptome by Quantitative Real-Time RT-PCR
This project aims to enhance the Arabidopsis community's available
expression data through the use of quantitative real-time RT-PCR methods
to profile all of the approximately 4,000 Arabidopsis genes for which
such data do not currently exist and to generate transgenic lines with
promoter-reporter (GFP/GUS) constructs of 1000 of these genes.
Brassica Comparative Genomics
As part of an effort to enhance Arabidopsis annotation, we performed whole genome
shotgun of Brassica oleracea and provide a searchable database of sequences. We
are also doing some targeted BAC sequencing of Brassica oleracea. For details,
please go to our Brassica oleracea Genome Database.
Arabidopsis thaliana Gene Index (AtGI)
All publicly available Arabidopsis ESTs as well as transcripts from GenBank have been assembled into contigs and built into the Arabidopsis thaliana Gene
Index (AtGI).
Ceres-TIGR Collaboration
In December, 2000, Ceres, Inc. provided 5,000 full-length cDNA sequences to
the TIGR annotation pipeline. You may retrieve the sequences from our ftp
site.
Landsberg erecta random sequence database
As part of our Arabidopsis Genome Program, we generated sequence from several
thousand random clones from the Landsberg erecta accession of Arabidopsis
thaliana. These sequences can be used to generate 'electronic polymorphisms'
that can be used to generate new, targeted markers for use in mapping studies.
BAC Sequencing at TIGR
As part of the AGI, TIGR was one of the three US groups funded to sequence the
Arabidopsis genome. The sequencing project is officially ended and all annotated
sequences are now part of the Arabidopsis thaliana Annotation Database.
BAC End Sequence Database
Over 40,000 BAC end sequences generated at TIGR, Genoscope, and U. Penn can be searched by clone name or sequence.
A FAQ for this site
Currently contains information on ordering BAC clones, EST clones, and map information.
Arabidopsis links
Links to Information on the Arabidopsis Genome available from other sites, including other AGI labs.
| This material is based upon work supported by the National Science Foundation under Grant No. 9813586. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do no
t necessarily reflect the views of the National Science Foundation. |  |
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