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Sample GSM2341972 Query DataSets for GSM2341972
Status Public on Jul 24, 2017
Title ES_OHT PRDM15KO 3 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) 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 SAMN05897901
SRA SRX2239201

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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