|
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 |
E-mail(s) |
biren@ucsd.edu
|
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] |
|
Relations |
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 |