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Sample GSM723767 Query DataSets for GSM723767
Status Public on Jul 01, 2012
Title RenLab-RNA-Seq-bone-marrow
Sample type SRA
Source name Mouse bone marrow
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 SRX062997
BioSample SAMN00618942
Named Annotation GSM723767_RenLab-RNA-Seq-bone-marrow-ZY24.bigwig
Named Annotation GSM723767_RenLab-RNA-Seq-bone-marrow-ZY26.bigwig

Supplementary file Size Download File type/resource
GSM723767_RenLab-RNA-Seq-bone-marrow-ZY24.bam 510.2 Mb (ftp)(http) BAM
GSM723767_RenLab-RNA-Seq-bone-marrow-ZY24.bigwig 27.7 Mb (ftp)(http) BIGWIG
GSM723767_RenLab-RNA-Seq-bone-marrow-ZY26.bam 529.7 Mb (ftp)(http) BAM
GSM723767_RenLab-RNA-Seq-bone-marrow-ZY26.bigwig 25.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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