Dataset mE_mRNA_L3_PS7-9

General Information
Name	mE_mRNA_L3_PS7-9	Species	D. melanogaster
Dataset type	RNA-Seq transcriptome coverage	FlyBase ID	FBlc0000103
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 third instar - cleared gut stage organism (Graveley et al., 2010.03.15) Comment:indicated as puff stage 7-9
Cell Line
Recent Updates
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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 late third instar larvae (puff stage 7-9, late wandering to puparium formation). 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	66,802,321 (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 and later L3 stages were then cultured in food supplemented with 0.05% bromophenol blue to mark the guts of feeding animals. Wandering larvae at puff stages 7-9 were marked by a clear gut. (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_2912 modMine: modENCODE_574 modMine: modENCODE_2912
Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	BS203 L3_PS7-9 (Graveley et al., 2010.03.15, Graveley, 2011.1.5, FBrf0212803) L3 blue PS(7-9) mE_mRNA_L3_PS7-9 modENCODE_2262 (Graveley et al., 2010.03.15) modENCODE_2912 (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]