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Sample GSM1407414 Query DataSets for GSM1407414
Status Public on Nov 19, 2014
Title Del_SCR_129_37 [Illumina MiSeq]
Sample type SRA
Source name embryonic stem cells
Organism Mus musculus
Characteristics strain: 129/Cast
genotype: ΔSCR(129), clone 37
passage: 5 after colony seletion
Treatment protocol SCR deleted clones contain a deletion of the Sox2 downstream enhancer which lies between Chr3:34653922-34661217 in the M. musculus genome build mm9. Deletions were generated in F1 ES cells using gRNA104 (TAGCATACGTCACGCCGGAA) and gRNA112 (ACTGTTCTCGAACACTCTGT) to target the Cas9 nuclease.
Growth protocol All cells were maintained on gelatin-coated plates in ES media supplemented with LIF and two inhibitors (2i, CHIR99021 and PD0325901).
Extracted molecule total RNA
Extraction protocol RNA was isolated using Trizol (Life Technologies) and DNase treated prior to library construction.
NEBNext mRNA Library Prep Reagent Set for Illumina
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Description Del_SCR_129_37.bedgraph
Data processing Variant sequence data was obtained from the Sanger Institute ( on 14/02/2014
Reads were aligned to in silico constructed versions of the 129S1 and CastEiJ genomes using Tophat2 running Bowtie2.
Mapped reads were split into 129, Cast or unknown using custom scripts and variant data, only variant bases sequenced with Phred score > 20 (on standard 33 offset) were considered for allele calling
BedGraphs were generated using bedtools v2.17.0 genomecov script with standard settings.
genome build:mm9
Submission date Jun 09, 2014
Last update date May 15, 2019
Contact name Jennifer Mitchell
Phone 4169786711
Organization name University of Toronto
Department Cell and Systems Biology
Street address 25 Harbord Street
City Toronto
State/province Ontario
ZIP/Postal code M5S 3G5
Country Canada
Platform ID GPL16417
Series (1)
GSE58339 A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential
BioSample SAMN02848490
SRA SRX583668

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

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