Green Lab confirmed introns 2008-12-02 set 2

C. elegans Intron Identification set.20090106.2_3_2_2_4_3_3_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

Reagents

  1. Animals: Caenorhabditis elegans, Mixed Larval Stages Grown for 4-5 Days, N2, N2
Release Date: 2009-01-28