General Information
Name
modENCODE_mRNA-Seq_treatments
Species
D. melanogaster
Project type
FlyBase ID
FBlc0000236
Parent Project
Data Provider
[modENCODE: Drosophila transcriptome](http://www.modencode.org/celniker/)
Title
Transcriptional profile of D. melanogaster response to various treatments, stranded RNA-Seq, modENCODE.
Overview
Description
An additional 6 RNA-Seq treatments samples have been added to this set.
Umbrella record for 21 collections that differ by treatment conditions from Oregon-R animals. Consists of 76-100nt strand-specific paired-end reads; longer reads trimmed so that all aligned reads are 76nt. Transcriptome represented as frequency of reads along genome (data in wiggle format; see GBrowse presentation). The profiles are represented as uniquely aligned reads.
Reagent type
Key genes
GO term(s)
SO term(s)
Details
Sample preparation
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 Compound-Based Treatments Profile](http://intermine.modencode.org/release-33/experiment.do?experiment=Transcriptional+Profiling+of+Compound-based+treatments+of+D.+melanogaster+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 (4)
Reported As
Symbol Synonym
Drosophila transcriptome
environmental perturbations
modENCODE_mRNA-Seq_treatments
Name Synonyms
Transcriptional profile of D. melanogaster response to various treatments, stranded RNA-Seq, modENCODE.
Secondary FlyBase IDs
    References (6)