GSE36025
GSE36025: Long RNA-seq from ENCODE/Cold Spring Harbor Lab
Summary:         These tracks were generated by the ENCODE Consortia. They contain information about mouse RNAs > 200 nucleotides in length obtained as short reads off the Illumina platform. Data are available from biological replicates.  Overall Design: Tissue Samples: Individual tissues were harvested from mouse strain C57BL/6NJ at different timepoints according to ENCODE cell culture protocols. Whenever possible biological replicates from litermates.Library Preparation: The published cDNA sequencing protocol was used. This protocol generates directional libraries and reports the transcripts' strand of origin. Exogenous RNA spike-ins were added to each endogenous RNA isolate and carried through library construction and sequencing. The spike-in sequence and the concentrations are available for download in the supplemental directory.Sequencing and Mapping: The libraries were sequenced on the Illumina platform (either GAIIx or Hi-Seq) in mate-pair fashion (either pair-end 76 or pair-end 101) to an average depth of 100 million mate-pairs. The data were mapped against hg19 using Spliced Transcript Alignment and Reconstruction (STAR) written by Alex Dobin (CSHL). More information about STAR, including the parameters used for these data, is available from the Gingeras lab.Verification: FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated for annotated exons and Spearman correlation coefficients were computed. In general, Rho values are > .90 between biological replicates.