Open Close
General Information
Name
modENCODE_mRNA-Seq_cell.A
Species
D. melanogaster
Project type
FlyBase ID
FBlc0000116
Parent Project
Data Provider
[modENCODE: Drosophila transcriptome](http://www.modencode.org/celniker/)
Title
Transcriptional profile of D. melanogaster cell lines, unstranded RNA-Seq, modENCODE.
Overview
Description

Umbrella record for numerous cell-culture RNA-Seq collections. Transcriptome represented as frequency of 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 Oligotex kit, then fragmented using divalent cations under elevated temperature. First and second strand cDNA synthesis was primed with random hexamers. The cDNA fragments were end-repaired using T4 DNA polymerase and Klenow DNA polymerase, and phosphorylated at their 5' ends with T4 polynucleotide kinase. After adding A bases to the 3' end of the DNA fragments, Illumina adaptor oligonucleotides were ligated to the ends and ~ 300 bp fragments were isolated from an agarose gel, enriched by PCR amplification, 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
Comments
Files
Additional Information

Unstranded Cell Line Transcriptional Profiling Using Illumina poly(A)+ RNA-seq(http://intermine.modencode.org/query/experiment.do?experiment=Unstranded+Cell+Line+Transcriptional+Profiling+Using+Illumina+poly%28A%29%2B+RNA-seq)

Synonyms and Secondary IDs (3)
Reported As
Symbol Synonym
Drosophila transcriptome
modENCODE_mRNA-Seq_cell.A
Name Synonyms
Transcriptional profile of D. melanogaster cell lines, unstranded RNA-Seq, modENCODE.
Secondary FlyBase IDs
    References (3)