General Information
Name
modENCODE_mRNA-Seq_cell.B
Species
D. melanogaster
Project type
FlyBase ID
FBlc0000260
Parent Project
Data Provider
[modENCODE: Drosophila transcriptome](http://www.modencode.org/celniker/)
Title
Transcriptional profile of D. melanogaster cell lines, stranded RNA-Seq, modENCODE.
Accessions
Overview
Description
Umbrella record for 24 cell lines. Consists of 76nt strand-specific single- or paired-end reads; transcriptome represented as frequency of strand-specific reads along genome (data in wiggle format; see GBrowse presentation). The profiles are represented as uniquely aligned reads.
Project attributes
Reagent type
Key genes
GO term(s)
SO term(s)
Details
Sample preparation
Cells were maintained between 2E6 and 1E7 cells/mL, and were harvested at about 5E6 cells/mL.
Protocol
Total RNA was isolated using Trizol, then Qiagen RNeasy spin columns. mRNA was isolated using Dynal oligo(dT) beads, then fragmented using divalent cations under elevated temperature, followed by sequential ligation of RNA linkers to the 5’ and 3’ ends. Next, reverse transcription was performed using a primer complementary to the 3’ linker and PCR was performed using primers complementary to both linkers. ~ 300 bp fragments were isolated from an agarose gel and gel-purified again.
Mode of Assay
The samples were quantitated using a Nanodrop, and loaded onto a flow cell for cluster generation and sequenced on an Illumina Genome Analyzer II using either single read or paired end protocols (Illumina).
Data analysis
Reads were aligned to Dmel_Release_6 using the STAR aligner v2.3.0e (Linux x86_64) with default parameters on the FASTQ files to generate multiply-mapped BAM files. These were filtered to include reads with only 1 aligned hit ( NH:i:1 attribute) to generate uniquely-mapped BAM files. A custom script was used to convert BAM files into bedgraph files (bam2bedgraph.cc).
Comments
Additional Information
[modENCODE Cell Lines Profile](http://intermine.modencode.org/release-33/experiment.do?experiment=Transcriptional+Profiling+of+D.+melanogaster+cell+lines+using+Illumina+poly%28A%29%2B+RNA-Seq)
The RNA-seq profiles displayed by FlyBase in GBrowse and used for RPKM calculation can be accessed at the FTP link below as .wig files. Please take note of how these FlyBase .wig files represent data for a contiguous sequence of bases with the same signal value. The value is declared only for the first position of that region, and applies to all positions that follow (these are not explicitly listed) until a new value at a new base position is declared.
Synonyms and Secondary IDs (2)
Reported As
Symbol Synonym
modENCODE_mRNA-Seq_cell.B
Name Synonyms
Transcriptional profile of D. melanogaster cell lines, stranded RNA-Seq, modENCODE.
Secondary FlyBase IDs
    References (7)