RNA-Seq windowed coverage

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


Using polyA+ RNA isolated from C. elegans N2, 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 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.

Series 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: RNA_isolation, Staging_and_isolation, RNA_isolation, Staging_and_isolation, Growth_condition_assay, Worm_growth
  2. Sample preparation: Sequencing, Sequencing
  3. Data Analysis: Alignment
    Growth Conditions:

Sample Details

  1. Animals/Lines: mid-L3, Male larva mid-L4 25dC 30 hrs post-L1, Adult spe-9(hc88) 23dC 8 days post-L4 molt, MT10430, mid-L2, early embryo, dauer entry daf-2(el370) 25dC 48 hrs post-L1, CB1370, dauer daf-2(el370) 25dC 91hrs post-L1, lin-35(n745) larva mid-L1 25dC 4.0 hrs post-L1, JK1107, dauer exit daf-2(el370) 25dC 91hrs 15dC 12hrs, BA671, mid-L4, late embryo 20dC 4.5 hours post-early embryo, CB4689, larva mid-L1 25dC 4.0 hrs post-L1, Young Adult, embryo him-8(e1480) 20dC, N2, CB1489
  2. External Links: SRX004866, SRX011569, SRX001874, SRX001872, SRX004867, SRX014008, SRX014010, SRX014007, SRX004865, SRX008140, SRX004868, SRX008139, SRX004864, SRX008138, SRX004869, SRX014006, SRX014009, SRX004863, SRX008136, SRX001875, SRX001873

Release Date: 2009-11-20