ML-DmD11, Multi mapper

Dm Cell Line Expression RNA-seq ML-DmD11 multiply mapping reads (Celniker project, Celniker subgroup)

Details

Stranded libraries were created from polyA+ RNA isolated from the D. melanogaster ML-DmD11 cell line, sequenced using Illumina GAIIx with single and/or paired-end modules, and aligned with TopHat against the r5 genome. Tracks show read alignments and density.
Total read count: 43270138
Mapped read count: 39991822
Alignment rate: 92%

General Description

RNA-seq analysis was performed on poly(A)+ RNA from D. melanogaster cell lines. Reads were sequenced on Illumina GAIIx were aligned to the D. melanogaster r5 genome using TopHat.

Protocols

  1. Data Analysis: TopHat stranded RNAseq alignment
  1. External Links: SRR070284, SRR070290, SRR111874

Related modENCODE submissions:


Release Date: 2012-01-11

poly(A)+ RNA was extracted from the cell line ML-DmD11, and libraries were constructed for Illumina paired-end sequencing. Resulting stranded short reads were aligned to the genome using TopHat. Tracks show read alignment density. Reads derived from the plus strand are on the positive y-axis; reads derived from the minus strand are on the negative y-axis.

General Description

RNA-seq analysis was performed on poly(A)+ RNA from 22 cell lines. 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 sequenced at the Brenton Graveley and Susan Celniker labs. Fastaq files were generated using the standard Illumina processing pipeline. Reads were aligned to the genome sequence using either Tophat v.1.1.2 (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).

Protocols

  1. Sample preparation: Stranded library prep
  2. Other Protocols: Paired-end Illumina Sequencing, Single-end Illumina Sequencing, TopHat alignment

Related modENCODE submissions:


Release Date: 2010-12-11 Submission 4420