|
| Status |
Public on Jun 02, 2016 |
| Title |
KH2.P14KO.b1 |
| Sample type |
SRA |
| |
|
| Source name |
KH2 mESCs
|
| Organism |
Mus musculus |
| Characteristics |
genotype: PRDM14 Knockout
cell line: KH2 embryonic stem (ES) cell line
|
| Growth protocol |
mESCs were grown in standard ESC medium containing Lif on a layer of feeder cells. Feeders were removed before TRIzol extraction.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was purified from cells with TRIzol (Invitrogen)
PolyA+ RNA was isolated using Dynabeads Oligo(dT)25 (Invitrogen) beads and converted into dsDNA using the dUTP method (Parkhomchuk et al., 2009). DNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR) using Q5 polymerase (NEB M0530) to generate strand-specific libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads mapped to mm9 with BOWTIE -m40 -v2
reads were assigned to the ENSEMBL annotation using DEGseq
Genome_build: mm9
Supplementary_files_format_and_content: Raw read count matching the ENSEMBL annotation
|
| |
|
| Submission date |
Aug 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Danny Reinberg |
| E-mail(s) |
reinbd01@nyumc.org
|
| Phone |
212-263-9036
|
| Organization name |
NYU School of Medicine / HHMI
|
| Street address |
522 First Avenue, 2nd floor Rm 211
|
| City |
New York City |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE71674 |
A Co-repressor CBFA2T2 regulates pluripotency and germline development [RNA-seq] |
| GSE71676 |
A Co-repressor CBFA2T2 regulates pluripotency and germline development |
|
| Relations |
| BioSample |
SAMN03952752 |
| SRA |
SRX1131583 |
