Embryo 2-4h RNA-Seq Multi mapper

Dm embryos, 2-4 hr after egg laying RNA-Seq, multi mappers (Celniker project)


RNA-seq was performed on a single biological sample of D. melanogaster (y cn bw sp) 2-4h embryos, using a combination of single- and paired-end sequencing. Sequences were aligned to the FlyBase r5 genome using TopHat. Track displays alignment read density.
Uniquely mapped reads: 65969646
Multiply mapped reads: 612539
Total reads sequenced: 79604482

General Description

RNA-seq analysis was performed on poly(A)+ RNA from 30 developmental stages spanning the life cycle of D. melanogaster, from 0-2hr embryos through 30-day male and female adults. Total RNA was isolated by the Peter Cherbas group. Isolation of poly(A)+ RNA and library construction were performed in the Brenton Graveley lab. Libraries were distributed among 5 labs in the Drosophila Transcriptome group for sequencing. The Susan Celniker lab performed paired-end sequencing exclusively (2x76 nt) . The Brenton Graveley, Tom Gingeras and Michael Brent labs performed single-end sequencing exclusively (1x76 nt). The Brian Oliver lab performed both single- and paired-end sequencing. All labs used the same Illumina GAII platform and called bases using the Illumina processing pipeline. Fastq files were generated using pipeline version 1.3 before 5/07/09 and using version 1.4 after that date. Reads were aligned to the genome sequence using Tophat v.1.0.10.


  1. Growth and isolation: mRNA purification from total RNA Sample prep
  2. Other Protocols: Paired-end Illumina Sequencing Single-end Illumina Sequencing TopHat alignment

Sample Details

  1. Samples: Celniker/RNA:218
  2. External Links: SRR023502 SRR023660 SRR023705 SRR023722 SRR023745 , and 11 more.

Related modENCODE submissions:

Release Date: 2010-06-10