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Sample GSM1900999 Query DataSets for GSM1900999
Status Public on Jul 24, 2017
Title ES_ETOH 3 Serum/Lif
Sample type SRA
 
Source name mESCs cultured in SL
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: mESCs
passages: 25-36
genotype: PRDM15+/+
Treatment protocol EtOH
Growth protocol Serum+Lif
Extracted molecule polyA 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
 
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 02, 2015
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 SAMN04127816
SRA SRX1301525

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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