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Series GSE36026 Query DataSets for GSE36026
Status Public on May 10, 2012
Title RNA-seq from ENCODE/LICR
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 (Yin Shen mailto:y7shen@ucsd.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

Using RNA-Seq (Mortazavi et al., 2008), high-resolution genome-wide maps of the mouse transcriptome across multiple mouse (C57Bl/6) tissues and primary cells were generated.
 
Overall design Cells were grown according to the approved ENCODE cell culture protocols (http://genome.ucsc.edu/ENCODE/protocols/cell/mouse).
RNA-Seq
RNA samples from tissues and primary cells were extracted from Trizol® according to protocol (Invitrogen). PolyA+ RNA was purified with the Dynabeads mRNA purification kit (Invitrogen). The mRNA libraries were prepared for strand-specific sequencing as described previously (Parkhomchuk et al., 2009).
Sequencing and Analysis
Samples were sequenced on Illumina Genome Analyzer II, Genome Analyzer IIx and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA. Alignment to the mouse genome was performed using TopHat (Trapnell et al., 2009). Wig files were generated by TopHat and expression levels were calculated with Cufflinks (Trapnell et al., 2010).
Web link http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeLicrRnaSeq
 
Contributor(s) Shen Y, Ren B
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA66167
Submission date Feb 23, 2012
Last update date May 15, 2019
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 (22)
GSM929703 LICR_RnaSeq_BAT_adult-24wks (superseded by GSE93472)
GSM929704 LICR_RnaSeq_MEL_immortalized (superseded by GSE93471)
GSM929705 LICR_RnaSeq_BMDM_adult-8wks (superseded by GSE93473)
Relations
SRA SRP013003

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
GSE36026_RAW.tar 2.0 Gb (http)(custom) TAR (of BIGWIG)
GSE36026_run_info.txt.gz 1.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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