early embryo

C. elegans early embryo N2 RNA-Seq sequences and alignments (Waterston project, Waterston subgroup)


Using polyA+ RNA isolated from C. elegans N2 early embryos, we prepared and sheared double-stranded cDNA. A ~200 bp fraction was isolated and used to generate libraries for massively parallel sequencing on the Illumina instrument (36 bp reads). Using maq and cross_match, we aligned the reads to the WS170 genome and to splice junction and splice leader databases. Raw alignments show positions of uniquely mapping reads. Raw coverage files represent depth of coverage of read alignments. Windowed coverage represents the sum of the read coverage in a 51bp window surrounding each base. Alignments and coverage files were lifted over to WS190 coordinates by the DCC for display in the browser.

General Description

Using massively parallel sequencing by synthesis methods, we are surveying transcripts from various stages, tissues and conditions of the nematode C. elegans. We use novel statistical approaches to evaluate coverage of annotated features of the genome and of candidate processed transcripts. We then provide lists of evidence of level of expression per transcript and catalogs of confirmed splice junctions, trans-spliced leader sequences, start sites, end sites, and poly-adenylation tracts for each stage/tissue/condition.


  1. Growth and isolation: Worm_growth, Staging_and_isolation, RNA_isolation
  2. Sample preparation: Sequencing
  3. Data Analysis: Alignment
  1. Growth Conditions: 25 degrees celsius

Sample Details

  1. Animals/Lines: early embryo, N2
  2. External Links: SRX004863, SRX004864

Release Date: 2009-10-28