Green Lab ESTs 2008-12-02 set 4

C. elegans Intron Identification set.20090106.2_3_2_2_3_2_2_2_2 (Waterston project, Green subgroup)

General Description

This experiment identifies intron boundary coordinates 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 unconfirmed by these alignments are tested for confirmation using RT-PCR, DNA sequencing, and sequence alignment. These PCR experiments use gene-specific/gene-specific, 5' RACE/gene-specific, and gene-specific/3' RACE primer pairs.

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:1902857087, TA:1902857088, TA:1902857089, TA:1902857090, TA:1902857091, TA:1902857092, TA:1902857093 , and 7115 more.


Release Date: 2009-11-17