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.
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).
Related modENCODE submissions:
Release Date: 2010-06-28