|
| Status |
Public on Apr 25, 2014 |
| Title |
CME185_Klf4OE_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
mouse ESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Undifferentiated mouse ESCs
cell line: CGR8
chip antibody: Klf4
|
| Treatment protocol |
None
|
| Growth protocol |
ES cells were grown with in standard media composed of DMEM supplemented with ES qualified FBS and Leukemia Inhibitory Factor (LIF). Cells overexpressing Klf4 or Klf5 were grown in the same media but without LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and formaldehyde was inactivated by the addition of 125 mM glycine. Chromatin from each cell line was sonicated to a length of around 250-500bp and immunoprecipitated using custom made antibodies provided bu Huck-Hui Ng. Samples were sequenced using the SOLEXA platform.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
ChIP-Seq reads were aligned using the Eland software to NCBI build 37 (mm9) of the mouse genome.
The MACS program (version 1.4) was used to detect peaks of ChIP enrichment. It was run with the default settings using a tag size of 35 and band width 280.
Genome_build: mm9
Supplementary_files_format_and_content: bed format. Chrom, ChromStart, ChromEnd, Name and Score.
|
| |
|
| Submission date |
Feb 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Irene Aksoy |
| E-mail(s) |
irene.aksoy@inserm.fr
|
| Organization name |
Stem Cell and Brain Research Institute
|
| Street address |
18 avenue du Doyen Lepine
|
| City |
Lyon |
| ZIP/Postal code |
69500 |
| Country |
France |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE49848 |
Genome-wide mapping of Klf4 and Klf5 in pluripotent mouse embryonic stem cells (ESCs) |
|
| Relations |
| BioSample |
SAMN02639641 |
| SRA |
SRX468969 |
