Green Lab ESTs SL Set 1

C. elegans SL Acceptor Site Identification set.20100203.2_3_2_2_4_3_3_2_3_3.ws180 (Waterston project, Green subgroup)

General Description

This experiment identifies splice leader acceptor sites in C. elegans genomic sequence. Initially, we run genefinder to predict protein-coding transcripts from the C. elegans chromosome sequences. We align existing cDNA and EST sequences to the predicted transcript sequences to confirm the transcript structure. Predicted splice junctions near the 5' transcript end that are unconfirmed by these alignments are tested for confirmation using 5' RACE, DNA sequencing, and sequence alignment. The resulting reads are aligned to the WS170 genomic sequences, the splice leader sequences, and the 5' RACE primer sequence. Combinations of the read-genomic and read-splice leader alignments are used to identify splice leader acceptor sites.

Protocols

  1. Growth and isolation: Organism_Preparation, RNA_Extraction
  2. Sample preparation: CDNA_Preparation, PCR, DNA_Sequencing
  3. Data Analysis: Basecalling, Alignment, Analysis

Sample Details

  1. Animals/Lines: Caenorhabditis elegans, Mixed Larval Stages Grown for 4-5 Days, N2
  2. External Links: TA:1971697210, TA:1971697211, TA:1971697214, TA:1971697217, TA:1971697249, TA:1971697251, TA:1971697256, and 9098 more.

Release Date: 2010-02-08