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Series GSE36025 Query DataSets for GSE36025
Status Public on Apr 02, 2012
Title Long RNA-seq from ENCODE/Cold Spring Harbor Lab
Project Mouse ENCODE
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Carrie Davis mailto:davisc@cshl.edu (experimental), Roderic Guigo mailto:rguigo@imim.es and lab (data processing) and Tom Gingeras mailto:gingeras@cshl.edu (primary investigator)). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

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.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
 
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.
Web link http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeCshlLongRnaSeq
 
Contributor(s) Davis C, Guigo R, Gingeras T
Citation(s) 25413365, 25582907
BioProject PRJNA66167
Submission date Feb 23, 2012
Last update date Feb 26, 2020
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (30)
GSM900183 CSHL_RnaSeq_Ovary_adult-8wks (superseded by GSE90190)
GSM900184 CSHL_RnaSeq_MammaryGland_adult-8wks (superseded by GSE90189)
GSM900185 CSHL_RnaSeq_Stomach_adult-8wks (superseded by GSE90192)
Relations
SRA SRP012040

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE36025_RAW.tar 43.2 Gb (http)(custom) TAR (of BAM, BEDRNAELEMENTS, BIGWIG)
GSE36025_run_info_with_UCSC_objects.txt.gz 6.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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