|
| Status |
Public on Jul 24, 2017 |
| Title |
ES_OHT PRDM15KO 2 2i |
| Sample type |
SRA |
| |
|
| Source name |
mESCs cultured in 2i+LIF
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: mESCs
passages: 25-36
genotype: PRDM15-/-
|
| Treatment protocol |
OHT (50nM)
|
| Growth protocol |
2i+Lif
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
fpkms_2i.txt
|
| Data processing |
The sequenced reads were mapped to mm9 build of the mouse genome using TopHat version 1.1.4 with the aligner Bowtie 0.12.7 with their default parameters except –m 1 and –segment-mismatches 2.
The mapped reads were further manipulated by removing the reads that mapped to multiple locations (-q 0) using SAMtools
FPKMs were calculated by Cufflink (2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Oct 11, 2016 |
| Last update date |
Apr 17, 2020 |
| Contact name |
Jingxian Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
|
| Department |
IMCB
|
| Street address |
61 Biopolis Drive Proteos
|
| City |
Singapore |
| State/province |
Singpaore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE73693 |
Whole transcriptome sequencing of WT and PRDM15KO mESCs |
| GSE73694 |
PRDM15 safeguards naïve pluripotency by transcriptionally regulating WNT and MAPK/ERK signaling |
|
| Relations |
| BioSample |
SAMN05897902 |
| SRA |
SRX2239200 |
