|
| Status |
Public on Oct 14, 2013 |
| Title |
EB_d6_shKdm5b |
| Sample type |
SRA |
| |
|
| Source name |
shKdm5b EB day 6
|
| Organism |
Mus musculus |
| Characteristics |
cell line: R1
cell type: embryonic stem
|
| Growth protocol |
ES cells were cultured on irradiated MEFs in DMEM, 15% FBS media containing LIF (ESGRO) at 37oC with 5% CO2. For ChIP experiments ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin. For embryoid body (EB) formation, ES cells were cultured in low attachment binding dishes to promote 3D formation in ES cell media without LIF.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvest using RNeasy and miRNeasy Qiagen kits.
Double-stranded cDNA was sonicated and end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-Seq
|
| Data processing |
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
Sequence reads were obtained and mapped to the mouse (mm8) genomes with Bowtie (0.12.7). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries). See BED files included in this submission.
The RPKM measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.
Genome_build: mm8
|
| |
|
| Submission date |
May 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin L Kidder |
| E-mail(s) |
[email protected]
|
| Organization name |
Wayne State University
|
| Department |
Oncology
|
| Lab |
Laboratory of Epigenomics
|
| Street address |
4100 John R St
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE46893 |
Extended self-renewal and accelerated reprogramming in the absence of Kdm5b |
| GSE47124 |
Extended self-renewal and accelerated reprogramming in the absence of Kdm5b [RNA-Seq] |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN02152315 |
| SRA |
SRX283860 |
