A data warehouse for the modENCODE project
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|experiment: Developmental Stage Timecourse Transcriptional Profiling with RNA-Seq||project: The Drosophila Transcriptome||PI: Sue Celniker||Labs: Sue Celniker|
|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).|