Embryo 4-6h RNA-Seq Multi mapper

Dm embryos, 4-6 hr after egg laying RNA-Seq, multi mappers (Celniker project, Gingeras subgroup)

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 Tophat v.1.0.10.

Protocols

  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:224
  2. External Links: SRR023539 SRR023669 SRR023696 , and 56 more.

Related modENCODE submissions:


Release Date: 2010-06-09