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Sample GSM1382216 Query DataSets for GSM1382216
Status Public on Jun 04, 2014
Title mEpiSC_Dnase
Sample type SRA
 
Source name Epiblast stem cells
Organism Mus musculus
Characteristics cell line: EpiSC9
Growth protocol mEpiSCs were cultured in Knockout DMEM supplemented with 20% KSR, 10ng/ml FGF2 (R&D Systems), 2mM Glutamax, 1x non-essential amino acids, and 0.1mM 2-mercaptoethanol and passaged every third day using 1.5 mg/ml collagenase type IV (Invitrogen) and trituration into small clumps of ~10-100 cells. Irradiated mouse embryonic fibroblasts (MEFs) served as a feeder layer for all pluripotent cell types and were maintained with DMEM supplemented with 10% fetal bovine serum, 2 mM glutamax, 1x non-essential amino acids, and 0.1 mM 2- mercaptoethanol. All cells were grown on Nunclon Δ-treated dishes or multiwell plates (Fisher Scientific) coated for 2 hours at 37°C with 0.1% (w/v) porcine gelatin (Sigma).
Extracted molecule genomic DNA
Extraction protocol 1x10^7 cells were subjected to DNase sequencing as previously described (Song et al., 2011).
Sequencing libraries were prepared as previously described (Song et al., 2011)
 
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina HiSeq 2000
 
Data processing The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) was used to remove adapter sequences and trim read ends using a quality score cutoff of 20.
DNase-seq data were aligned to mm9 genome assemblies (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Bowtie v0.12.9 (Langmead et al., 2009), allowing reads with ≤ 2 mismatches and randomly assigning reads with > 1 reportable alignment to one alignment site ("-M 1" parameter).
Peaks were detected with MACS v1.4 (Zhang et al., 2008).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files - Wiggle tracks stepped at 25 bp were generated by MACS, normalized to the median signal by chromosome and converted to bigwig format using the UCSC Genome Browser’s wigToBigWig utility (retrieved from http://hgdownload.cse.ucsc.edu/admin/exe/). bed files - MACS called peaks.
 
Submission date May 07, 2014
Last update date May 15, 2019
Contact name Paul J. Tesar
E-mail(s) paul.tesar@case.edu
Organization name Case Western Reserve University School of Medicine
Department Genetics and Genome Sciences
Street address 10900 Euclid Ave
City Clev
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL13112
Series (2)
GSE57406 Epigenomic comparison of distinct pluripotent stem cell states reveals a new class of enhancers with roles throughout mammalian development (DNase-seq)
GSE57409 Epigenomic comparison of distinct pluripotent stem cell states reveals a new class of enhancers with roles throughout mammalian development
Relations
BioSample SAMN02767298
SRA SRX535237
Named Annotation GSM1382216_mEpiSC_DNase.bigWig

Supplementary file Size Download File type/resource
GSM1382216_mEpiSC_DNase.bed.peak.txt.gz 1.0 Mb (ftp)(http) TXT
GSM1382216_mEpiSC_DNase.bigWig 299.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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