General Information
Name
BCM_1_RNAseq
Species
D. melanogaster
Project type
FlyBase ID
FBlc0000060
Parent Project
    Data Provider
    Title
    Developmental time course of D. melanogaster transcriptome, RNA-Seq, Baylor College of Medicine.
    Overview
    Description
    Umbrella record for 12 collections that differ by developmental stage, from embryos to aged adults. Transcriptome represented as frequency of reads along genome (see GBrowse presentation; data in wiggle format). RNA junctions identified and characterized (presented in GBrowse and in RNA junction reports).
    Reagent type
    Key genes
    GO term(s)
    SO term(s)
    Details
    Sample preparation
    Protocol
    Whole body samples were homogenized in 1ml of Trizol per 50-100 mg of tissue to isolate total RNA. Polyadenylated mRNA was then isolated from 20ug total RNA using an mRNA Purification Kit (Invitrogen). Double-stranded cDNA was made using Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and random hexamer primers. Size fractionated 200-400bp cDNAs were used for Solexa library construction (paired end layout).
    Mode of Assay
    The cDNA library was characterized by high-throughput sequencing (Illumina GAII).
    Data analysis
    Reads were aligned to the Drosophila reference genome (Dmel_Release_5) using BLAT. The BLAT ooc file was prepared with -repMatch=128 and otherwise default parameters were used. Paired reads were parsed to disambiguate multiple alignment locations if one of the two pairs mapped uniquely or the pair agreed on a unique mapping location. Reads with unaligned mates or pairs which did not agree were treated as single-end reads. Only reads with unique alignment location were considered for analyses.
    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.
    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".
    Files
    Additional Information
    Synonyms and Secondary IDs (3)
    Reported As
    Symbol Synonym
    BCM_1_RNAseq
    Name Synonyms
    Developmental time course of D. melanogaster transcriptome, RNA-Seq, Baylor College of Medicine.
    Secondary FlyBase IDs
      References (4)