|
| Status |
Public on Jul 01, 2012 |
| Title |
RenLab-RNA-Seq-kidney |
| Sample type |
SRA |
| |
|
| Source name |
Mouse kidney
|
| 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 Genome Analyzer II |
| |
|
| Data processing |
fastq: Illumina's Genome Analyzer Pipeline
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 |
GPL9250 |
| 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 |
SRX063001 |
| BioSample |
SAMN00618946 |
| Named Annotation |
GSM723771_RenLab-RNA-Seq-kidney-ZY15.bigwig |
| Named Annotation |
GSM723771_RenLab-RNA-Seq-kidney-ZY16.bigwig |
