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Sample GSM723776 Query DataSets for GSM723776
Status Public on Jul 01, 2012
Title RenLab-RNA-Seq-mESC
Sample type SRA
Source name Bruce4 embryonic stem cells
Organism Mus musculus
Characteristics strain: C57Bl/6
Treatment protocol None
Growth protocol Adult liver, kidney, bone marrow, lung, heart, cortex, cerebellum, spleen were dissected from 8-week old male C57Bl/6 mice (Charles River). Mouse embryonic fibroblast (MEF) MEF cells were derived from E13.5 C57Bl/6 mouse embryos and genotyping was performed to select male MEF cells used for this study. mESC line Bruce4 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments.
Extracted molecule polyA RNA
Extraction protocol 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 in Parkhomchuk, D. et al. (2009).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing fastq: Illumina's HiSeq Control Software
bam and bigWig: Alignment to mm9 using TopHat with default parameters.
Submission date May 13, 2011
Last update date May 15, 2019
Contact name Bing Ren
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platform ID GPL13112
Series (2)
GSE29184 A draft map of cis-regulatory sequences in the mouse genome
GSE29278 A draft map of cis-regulatory sequences in the mouse genome [RNA-Seq]
Reanalyzed by GSE80797
SRA SRX063006
BioSample SAMN00618951
Named Annotation GSM723776_RenLab-RNA-Seq-mESC-ZY27.bigwig
Named Annotation GSM723776_RenLab-RNA-Seq-mESC-ZY28.bigwig

Supplementary file Size Download File type/resource
GSM723776_RenLab-RNA-Seq-mESC-ZY27.bam 1019.3 Mb (ftp)(http) BAM
GSM723776_RenLab-RNA-Seq-mESC-ZY27.bigwig 88.8 Mb (ftp)(http) BIGWIG
GSM723776_RenLab-RNA-Seq-mESC-ZY28.bam 941.3 Mb (ftp)(http) BAM
GSM723776_RenLab-RNA-Seq-mESC-ZY28.bigwig 82.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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