Dataset mE_mRNA_L2

General Information
Name	mE_mRNA_L2	Species	D. melanogaster
Dataset type	RNA-Seq transcriptome coverage	FlyBase ID	FBlc0000099
Source & Content
Consists of	cDNA short sequencing reads from high-throughput sequencing. (Graveley et al., 2010.03.15)
Created by
Available from
Strain	iso-1 (Graveley et al., 2010.03.15)
Stage & tissue
Stage Tissue/Position (including subcellular localization) Reference second instar larval stage organism (Graveley et al., 2010.03.15)
Cell Line
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Description & Members
Description	Short sequencing reads of cDNA prepared from polyadenylated RNA isolated from second instar larvae. Transcriptome represented as frequency of reads along genome (see GBrowse presentation; data in wiggle format); this collection is composed of uniquely aligned reads. (Graveley et al., 2010.03.15)
Parent collections	modENCODE_mRNA-Seq_U
Component collection(s)
Number in collection	103,442,079 (Graveley et al., 2010.03.15)
Comment on number in collection	Uniquely aligned reads; as reported. (Graveley et al., 2010.03.15)
Members
Experimental protocol
Vector
Sample preparation	A 2 hour embryo collection was aged 20 hours. Larvae were allowed to feed until harvesting 66-70 hours after egg laying (AEL). (Graveley et al., 2011) See report for modENCODE_mRNA-Seq_U. (Graveley et al., 2010.03.15)
Collection preparation	See report for modENCODE_mRNA-Seq_U. (Graveley et al., 2010.03.15)
Mode of assay	Consists of a mixture of 75nt and 76nt reads; 76nt used by FlyBase for computation of expression levels (as RPKM). (Gelbart and Emmert, 2011.8.23) Read length (bases):76 (Gelbart and Emmert, 2011.8.23) See report for modENCODE_mRNA-Seq_U. (Graveley et al., 2010.03.15)
Assay platform	See report for modENCODE_mRNA-Seq_U. (Graveley et al., 2010.03.15)
Data analysis	See report for modENCODE_mRNA-Seq_U. (Graveley et al., 2010.03.15)
Additional data
	More information is available under: modENCODE dataset description: modENCODE_2910 modMine: modENCODE_574 modMine: modENCODE_2910
Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	BS111 L2 (Graveley et al., 2010.03.15, Graveley, 2011.1.5, FBrf0212803) mE_mRNA_L2 modENCODE_2258 (Graveley et al., 2010.03.15) modENCODE_2910 (Graveley et al., 2010.03.15)
Secondary FlyBase IDs

References ( 5 )
Supplementary material	Graveley et al., 2011, Nature 471(7339): Supplementary Information. [FBrf0213508]
Personal communication to FlyBase	Graveley, 2011.1.5, modENCODE RNA-Seq junction data modENCODE RNA-Seq junction data [FBrf0212682] Graveley et al., 2010.03.15, The D. melanogaster transcriptome: modENCODE RNA-Seq data The D. melanogaster transcriptome: modENCODE RNA-Seq data [FBrf0210195] modENCODE RNA-Seq junction data [FBrf0212803]
FlyBase analysis	Gelbart and Emmert, 2011.8.23, Calculation of RPKM to generate quantitative expression data: read-length values for modENCODE developmental timecourse RNA-Seq data. Calculation of RPKM to generate quantitative expression data: read-length values for modENCODE developmental timecourse RNA-Seq data. [FBrf0214760]