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Series GSE39524 Query DataSets for GSE39524
Status Public on Jul 20, 2012
Title RNA-seq from ENCODE/UW
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 (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track was produced as part of the mouse ENCODE Project. This track shows RNA-seq measured genome-wide in mouse tissues and cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType). Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types that also had corresponding DNase I hypersensitive profiles.

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 Cells were grown according to the approved ENCODE cell culture protocols. Fresh tissues were harvested from mice and stored until used for preparing total RNA samples. The total RNA was used as starting material to select poly-A RNA and used for constructing SOLiD libraries according to the protocols supplied by the manufacturer. All RNA samples were spiked in with NIST standards before libraries were constructed. The RNA-seq libraries were sequenced on ABI SOLiD sequencing platform as 50-base reads according to the manufacturer's recommendations.
Reads were aligned to the mm9 reference genome using ABI BioScope software version 1.2.1. Colorspace FASTQ format files were created using Heng Li's solid2fastq.pl script version 0.1.4 (Li et al., 2009a), representing 0, 1, 2, 3 color codes with the letters A, C, G, T respectively. Signal files were created from the BAM (Li et al., 2009b) alignments using BEDTools (Quinlan et al., 2010).
Web link http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwRnaSeq
 
Contributor(s) Sandstrom R
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA66167
Submission date Jul 20, 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 (1)
GPL10010 AB SOLiD System (Mus musculus)
Samples (25)
GSM970851 UW_RnaSeq_Liver_E14.5_129
GSM970852 UW_RnaSeq_Thymus_adult-8wks_C57BL/6
GSM970853 UW_RnaSeq_NIH-3T3_immortalized_NIH/Swiss
Relations
SRA SRP014923

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
GSE39524_RAW.tar 10.0 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data not provided for this record
Raw data are available in SRA
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