|
| Status |
Public on Jun 05, 2014 |
| Title |
Input_2i_Otx2_ChIP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells (ESC)
|
| Organism |
Mus musculus |
| Characteristics |
esc strain: R1 ESC
mouse strain: 129SV
antibody: none
|
| 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 |
SAMN02697979 |
| SRA |
SRX499144 |
