Dataset BCM_1_RNAseq_junctions

General Information
Name	BCM_1_RNAseq_junctions	Species	D. melanogaster
Dataset type	RNA-Seq transcriptome junctions	FlyBase ID	FBlc0000204
Source & Content
Consists of	cDNA short sequencing reads from high-throughput sequencing, junctions only. (Daines et al., 2011.3.30)
Created by
Available from
Strain	Canton-S (Daines et al., 2011.3.30)
Stage & tissue

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	Umbrella record for 12 collections that differ by developmental stage, from embryos to aged adults. RNA junctions identified and characterized (presented in GBrowse and in RNA junction reports). (Daines et al., 2011.3.30)
Parent collections	BCM_1_RNAseq
Component collection(s)	BCM_1_E2-4hr_junctions BCM_1_E14-16hr_junctions BCM_1_E2-16hr_junctions BCM_1_E2-16hr100_junctions BCM_1_L3i_junctions BCM_1_L3i100_junctions BCM_1_P3d_junctions BCM_1_FA3d_junctions BCM_1_MA3d_junctions BCM_1_P_junctions BCM_1_L_junctions BCM_1_A17d_junctions
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	See report for BCM_1_RNAseq. (Daines et al., 2011.3.30)
Collection preparation	See report for BCM_1_RNAseq. (Daines et al., 2011.3.30)
Mode of assay	See report for BCM_1_RNAseq. (Daines et al., 2011.3.30)
Assay platform	See report for BCM_1_RNAseq. (Daines et al., 2011.3.30)
Data analysis	See report for BCM_1_RNAseq. (Daines et al., 2011.3.30)
Additional data

Associated files
Additional sites
Comments
	A small number of junctions predicting very small and very long introns may be mispredictions and should be interpreted with care; these are currently being re-examined. (Daines et al., 2011.3.30) For ~1900 predicted junctions, the supporting evidence came from a methodology (Wang L, Xi Y, Yu J, Dong L, Yen L, et al. 2010 A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq. PLoS ONE 5(1): e8529. doi:10.1371/journal.pone.0008529) that did not report number of supporting junction-spanning reads. Each of these ~1900 predicted junctions was supported by at least two reads, and so we have noted these by having a total junction-spanning read count of ">1". However, we do not know which developmental stages these supporting reads were in, and so all developmental stages are reported as "0". (Daines et al., 2011.3.30)
Synonyms & Secondary IDs
Reported As
Symbol Synonym	BCM_1_RNAseq_junctions
Secondary FlyBase IDs

References ( 2 )
Research paper	Daines et al., 2011, Genome Res. 21(2): 315--324 The Drosophila melanogaster transcriptome by paired-end RNA sequencing. [FBrf0213064]
Personal communication to FlyBase	Daines et al., 2011.3.30, Addendum concerning analysis of RNA-Seq junctions Addendum concerning analysis of RNA-Seq junctions [FBrf0213348]