Cotton Fiber dbEST

General Description:

Cotton fiber ESTs were generated from 7-10 dpa fibers from the diploid species, Gossypium arboreum L. cv. AKA8401 as a main goal of our NSF Cotton Genome Project (DBI9872630). From 92,160 individual cDNA clones is arrayed in 240 X 384-well plates, over 50,000 fiber cDNA were sequenced and only quality-controlled ESTs (> 50 high quality nucleotides) released to GenBank. The UCD Ga Cotton Fiber dbEST consists of 46,603 EST sequences in a web-based, user-friendly database available for searching by the scientific community.

The dbEST consists of a Unigene (UG)/Non-redundant (NR) set of 13,947 quality-controlled consensus sequences that defines the cotton fiber transcriptome during rapid fiber elongation.

XGI GA fiber Cotton Contig Database
   XGI hosts fully searchable and annotated list of all of the GA fiber contigs and the ESTs that compose them. This list can be found here.
      XGI Cotton database
      Username: cotton1
      Password: cotton1

Conversion of EST IDs

In order to query the XGI cotton EST database, the GenBank EST IDs should be converted into XGI EST IDs following the guidelines:

For UCD Unigene/Non-redundant Ga Fiber EST Gene Index, click here.
   UCD Unigene/Non-redundant Ga Fiber EST Gene Index - Excel File

The Ga Cotton Fiber dbEST consists of four data sets:

• Ga_Ea (12,767)

  • Sequenced from the 5'-terminus before normalization

  • Only data set suitable for in silico expression analysis as sequencing took place before normalization

• Ga_Eb (13,613)

  • A subset of Ga_Ea ESTs sequenced from the 3'-terminus

• Ga_Ec (3,026)

  • Normalized

    75 Redundant Ea sequences (>6 transcripts/cluster) removed

• Ga_Ed (14,915)

  • Random sequencing of 9,388 cDNAs following second round of normalization

    Normalization removed redundant Ea and Eb sequences

  • Sequenced from both 5'- and 3'-termini