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Genelet Gap Closing

experiment: Genelet Gap Closing project: The C. elegans Transcriptome PI: Robert Waterston Labs: Phil Green
We identify gaps in RNAseq genelet data and run PCRs to bridge them. Using RNAseq aggregate integrated genelets, we construct a set of merged genelets from genelets that are not known single exon transcripts by forming the unions of genelets with overlapping exon bases. The terminal genelet features consisting of transcript start sites, SL acceptor sites, transcript end sites, and poly-A sites are assigned to a merged genelet with the genelets that compose it. For each chromosome and strand, we select candidate genelet pairs in which neither facing genelet end has an assigned terminal feature, the gap is up to 5000 bases long, and the genelet pair has average coverage per base of 50 or less where the genelet pair coverage is the value for the lower coverage genelet. After removing candidate pairs that are covered by existing data, we pick PCR primers for the remaining candidate pairs so that the product contains at least one known intron. The PCR products are sequenced from the PCR primers using a capillary DNA sequencing machine. We use phred to call bases and cross_match to align with splicing the resulting reads to the genomic sequence. Genelet gaps are considered to be closed when the alignments cover at least the genelet bases at the gap ends.

All features generated by this experiment:
Feature Export
Intron 3241 TAB CSV GFF3 (for UCSC) SEQ
EST 2973 TAB CSV GFF3 SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All 4 tracks I II III IV V X
All entries in public repositories generated by this experiment
There is 1 RTPCR submission for this experiment:
DCC id Name developmental stage strain Embargoed until Features, GBrowse and Data Files
modENCODE_3536

Intron Confirmations for Genelet Gap Closing 2011-03-24 Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
Intron: 3241   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
EST: 2973   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: Genelet_Gap_Closing
Genelet_Gap_Closing
Waterston_match_part_8561_3536
Waterston_intron_8561_3536
Trace Archive: 2298888440
Trace Archive: 2298888441
Trace Archive: 2298888442
Trace Archive: 2298888443
Trace Archive: 2298888444
...All entries in public repositories generated by this submission



1 files Download data files