Dataset modENCODE_mRNA-Seq_cell.A

General Information
Name	modENCODE_mRNA-Seq_cell.A	Species	D. melanogaster
Dataset type	RNA-Seq transcriptome profiles	FlyBase ID	FBlc0000116
Source & Content
Consists of	cDNA short sequencing reads from high-throughput sequencing. (Graveley et al., 2010.03.15)
Created by	modENCODE: Drosophila transcriptome
Available from
Strain
Stage & tissue

Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
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. (Graveley et al., 2010.03.15)
Parent collections
Component collection(s)	mE_CME-W1-cl.8+_polyA mE_Kc167_polyA mE_ML-DmBG3-c2_polyA mE_S2-DRSC_polyA
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	Cell culture and collection and preparation of total RNA samples described in modMine entry modENCODE_560 (link below). (Graveley et al., 2010.03.15)
Collection preparation	The poly(A)+ RNA was fragmented using divalent cations under elevated temperature, following by first and second strand cDNA synthesis 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. (Graveley et al., 2010.03.15)
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). (Graveley et al., 2010.03.15)
Assay platform	Illumina Genome Analyzer II (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL9061) (Graveley et al., 2010.03.15)
Data analysis	Bases were called using the Illumina processing pipeline. Image data were then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald. Fastaq files were generated using pipeline version 1.3 before 5/07/09 and using 1.4 after. Reads were aligned using Bowtie v0.10.0 to a combined index of the genome and both annotated and predicted splice junctions. Paired-end alignments were further parsed using Spliced-Paired-end-Aligner (SPA, written by Michael Duff) to identify the optimal mapping location for mate-pairs. (Graveley et al., 2010.03.15)
Additional data
	More information is available under: GEO: GSE15596 modENCODE: Drosophila transcriptome modMine: modENCODE_560
Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	Drosophila transcriptome (Graveley et al., 2010.03.15) modENCODE_mRNA-Seq_cell.A
Secondary FlyBase IDs

References ( 2 )
Research paper	Cherbas et al., 2011, Genome Res. 21(2): 301--314 The transcriptional diversity of 25 Drosophila cell lines. [FBrf0213077]
Personal communication to FlyBase	Graveley et al., 2010.03.15, The D. melanogaster transcriptome: modENCODE RNA-Seq data The D. melanogaster transcriptome: modENCODE RNA-Seq data [FBrf0210195]