Embryo 0-2h RNA-Seq Multi mapper

Dm embryos, 0-2 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) 0-2h 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: 69205082
Multiply mapped reads: 503208
Total reads sequenced: 100870337

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. Fastaq 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 either Tophat v.1.0.10 (to identify multiply-mapped reads) OR were aligned to the genome and a splice-junction database using Bowtie 0.9.9 (to identify only uniquely-mapped reads).


  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:212
  2. External Links: SRR023199 SRR023659 SRR023663 , and 75 more.

Related modENCODE submissions:

Release Date: 2010-06-28