Description
These tracks were generated by the
ENCODE
Consortium. They contain information about human RNAs greater than 200
nucleotides in length that were obtained as short reads from the Illumina GAIIx
platform. Data are available from biological replicates of several
cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from
whole cells, there are also data from various subcellular
compartments. In many cases, there are Cap Analysis of Gene
Expression (CAGE, see the
RIKEN CAGE Loc track),
Small RNA-seq (less than 200 nucleotides, see the
CSHL Sm RNA-seq track) and Pair-End
di-TAG-RNA (PET-RNA, see the
GIS RNA PET track) datasets available from the same 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. Specific column specifications can be found in the
supplemental directory.
- Signals
- The Plus Signal and Minus 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. See 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
Cell Culture
Cells were grown according to the approved
ENCODE
cell culture protocols.
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 Illumina PhiX
control library was also spiked-in at 1% to each completed human
library just prior to cluster formation.
Accompanying each RNA-seq dataset is a
Protocol document available for download as a PDF. This document contains details
about the RNA isolations and treatments, library construction,
spike-ins as well as quality control figures for individual libraries.
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 GAIIx platform
as paired-ends for 76 or 101 cycles for each read.
The average depth of sequencing was ~200 million reads
(100 million paired-ends).
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.
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 Gencode exons and Spearman values were compared.
In general, Rho values are greater than .90 between biological replicates.
Release Notes
This is release 3 (Sept 2012) of this track for hg19. It has no new experiments, but has
additional files for many experiments. The hMNC-CB experiment has been revoked. The
doubly compressed spike-ins files have been uncompressed.
The hMNC-PB experiment has been replaced with improved depth.
The current downloadable elements files (Transcripts, Genes and Exons) were generated
using GENCODE V10, while the older datasets were generated using GENCODE V7.
The "view" metadata will specify V7 or V10 for these files.
Errata
6/6/2013 - CSHL reports that one lane of reads is missing from the SK-N-SH-RA fastq read2 file
(wgEncodeCshlLongRnaSeqSknshraCellPapFastqRd2Rep1.fastq.gz).
Credits
These data were generated and analyzed by the transcriptome group led by
Tom Gingeras at
Cold Spring Harbor Laboratories and the laboratory of Roderic Guigo at
the
Center for Genomic Regulation (CRG) in Barcelona.
Contact:
Carrie Davis
References
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.
Publications
Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y et
al.
Understanding transcriptional regulation by integrative analysis of transcription factor binding
data.
Genome Res. 2012 Sep;22(9):1658-67.
Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR et al.
Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.
Nat Genet. 2011 Oct 23;43(12):1179-85.
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A,
Knowles DG et al.
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution,
and expression.
Genome Res. 2012 Sep;22(9):1775-89.
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R,
Birney E et al.
Modeling gene expression using chromatin features in various cellular contexts.
Genome Biol. 2012 Sep 5;13(9):R53.
ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M.
An integrated encyclopedia of DNA elements in the human genome.
Nature. 2012 Sep 6;489(7414):57-74.
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.
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.