NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1355168 Query DataSets for GSM1355168
Status Public on Jun 05, 2014
Title Oct4_EpiLC_minusActivin
Sample type SRA
 
Source name epiblast like cells (EpiLC)
Organism Mus musculus
Characteristics esc strain: R1 ESC
mouse strain: 129SV
antibody: Oct4 (Santa Cruz sc-8628)
Growth protocol All mouse ESC lines were adapted for a minimum of 5 passages to growth in serum free N2B27 based medium supplemented with MEK inhibitor PD0325901 (0.8μM) and GSK3β inhibitor CHIR99021 (3.3μM) in tissue culture dishes pretreated with 7.5μg/ml polyL-ornithine (Sigma) and 5μg/ml laminine (BD) (Hayashi et al., 2011). To induce EpiLC differentiation, cells were washed with PBS, trypsinized and strained. 200,000 to 300,000 cells per 10cm2 were plated on tissue culture dishes pretreated with 5μg/ml Fibronectin (Millipore) in N2B27 based medium supplemented with 1% KSR (Invitrogen) and 12μg/ml bFGF (Peprotech). Where indicated 20ng/ml Activin A (R&D Scientific) was added.
Extracted molecule genomic DNA
Extraction protocol cells were fixed with 1% Formaldehyde for 10 minutes, then quenched with 0.125M Glycine. After nuclei extraction as described in Rada et al, Nature 2011. Sonication was carried out using Diagenode bioruptor in 15ml Falcon tubes. Each ChIP was validated using q-PCR against selected loci.
libraries were prepared for Illumina sequencing using descibed protocols. All libraries were sequenced as single reads, 36bp length on the Illumina Genome Analyzer Iix.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Mouse embryonic stem cells grown under ESC (serum free, N2B27 based 2i+LIF) or differentiated to EpiLCs (serum free, N2B27 based, bFGF and KOSR) for 48h
Data processing libraries were sequenced with Illumina Genome Analyzer.
unique reads were mapped with bowtie to mm9.
wig files were created using QuEST software (Valouev et al, Nature Methods, 2008) using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: wig files of ChIP-seq reads
 
Submission date Mar 21, 2014
Last update date May 15, 2019
Contact name Christa Buecker
E-mail(s) cbuecker@stanford.edu
Organization name Stanford University
Department Chemical and Systems Biology
Lab Joanna Wysocka
Street address 269 Campus Drive
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
 
Platform ID GPL11002
Series (2)
GSE56098 Reorganization of enhancer patterns in transition from naïve to primed pluripotency (ChIP-seq)
GSE56138 Reorganization of enhancer patterns in transition from naïve to primed pluripotency
Relations
BioSample SAMN02697990
SRA SRX499128

Supplementary file Size Download File type/resource
GSM1355168_Oct4.AFK.noActA_normalized.profile.wig.gz 26.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap