Description

These tracks were generated by the ENCODE Consortium. They contain information about mouse RNAs greater than 200 nucleotides in length obtained as short reads off the Illumina platform. Data are available from biological replicates.

Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here.

To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide.

Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types and compartments.

Contigs

The Contigs represent blocks of overlapping mapped reads from the pooled biological replicates.

Raw Signals

The Plus Raw Signal and Minus Raw Signal views show the density of mapped reads on the plus and minus strands (wiggle format), respectively.

Alignments

The Alignments view shows individual reads mapped from biological replicates to the genome and indicates where bases may mismatch. Every mapped read is displayed, i.e. uncollapsed. The alignment file follows the standard SAM format of Bowtie output. See the Bowtie Manual for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format.

Splice Junctions

Subset of aligned reads that cross splice junctions. Specific column specifications can be found in the supplemental directory.

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

Additional views are available on the Downloads page.

Methods

Tissue Samples

Individual tissues were harvested from mouse strain C57BL/6J at different timepoints according to ENCODE cell culture protocols. Whenever possible, biological replicates were obtained from littermates.

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 mm9 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.

For each experiment, there are additional element data views data files available for download. These elements were assessed for reproducibility using a nonparametric irreproducible detection (IDR) rate script. The IDR values for each element are included in the files for end-users to use as a threshold. An IDR value of 0.1 means that the probability of detecting that element in a third experiment equivalent in depth to the sum of the bioreplicates is 90%. In addition, expression values for annotated genes, transcripts and exons were computed. Further explanation of these files is available for download in the supplemental directory.

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 greater than 0.90 between biological replicates.

Release Notes

This is release 3 (Sept 2012) of this track. It adds data for bladder, cerebellum, CNS, cortex, frontal lobe, limb, liver, placenta, and whole brain. The samples for CNS, liver, limb and whole brain vary over age (developmental stage). This release also contains replacement BAM files for the previous ones had the second read reverse complemented.

Credits

These data were generated and analyzed by the transcriptome group at Cold Spring Harbor Laboratories and the Center for Genomic Regulation (CRG in Barcelona), who are participants in the ENCODE Transcriptome Group.

Contacts: Carrie Davis (experimental), Roderic Guigo and lab (data processing), Tom Gingeras (primary investigator)

References

Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 2011 Sep;21(9):1543-51. PMID: 21816910; PMC: PMC3166838

Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Oct;37(18):e123. PMID: 19620212; PMC: PMC2764448

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here.