|
Status |
Public on Jul 24, 2017 |
Title |
ES_ETOH 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 |
EtOH
|
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) |
zhangjingxian.nus@gmail.com
|
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 |
SAMN05897905 |
SRA |
SRX2239197 |