|
| Status |
Public on Jun 22, 2021 |
| Title |
RNA-Seq DKO-B-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryoid bodies
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cell, Rx:GFP KI
genotype: Wdr5 and p53 double knockout
agent column: ESC differeantion using SFEBq method
|
| Treatment protocol |
For SFEBq differerentaton, 2% matrigel was added at EB day 1.
|
| Growth protocol |
Rx:GFP mESCs were maintained in 2i+LIF media and induced to differentiation with SFEBq method (5%KSR in GMEM media)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation and DNase treatment were according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.
Single end RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
DKO-B-rep1
|
| Data processing |
Reads from sample 5 - 10 were aligned to the mm10 genome assembly using hisat2 version 2.0.0
Reads from sample 1-4 and sample 11-18 were aligned to the mm10 genome assembly using STAR version 2.7.3a
transcript gtf files were calculated using cufflinks version 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: transcript gtf file.
|
| |
|
| Submission date |
Jun 21, 2021 |
| Last update date |
Jun 22, 2021 |
| Contact name |
Rajesh C Rao |
| E-mail(s) |
rajeshr@umich.edu
|
| Organization name |
University of Michigan
|
| Street address |
1000 Wall Street
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE178555 |
Transcriptome of Wdr5 and (or) p53 double knockout ESCs and embryoid bodies |
| GSE178556 |
Wdr5 |
|
| Relations |
| BioSample |
SAMN19796604 |
| SRA |
SRX11188281 |
