|
| Status |
Public on Dec 19, 2011 |
| Title |
KO HELLS |
| Sample type |
SRA |
| |
|
| Source name |
MEF
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E13.5
genotype/variation: E2f3-/-
cell type: mouse embryonic fibroblasts (MEF)
chip antibody: HELLS
|
| Growth protocol |
MEFs were cultured in DMEM (Dulbecco's modified Eagle's Medium) with 4.5 g/L glucose (Gibco) supplemented with 10% inactivated fetal calf serum (Gibco) and 1% penicillin/streptomycin (Gibco).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
100 million WT or E2f3-/- cells were lyzed and 10µg of antibody or µg IgG used (I5006; Sigma). The DNA was purified with a MinElute PCR Purification column (Qiagen) and eluted in 11 µl. All reagents used were supplied with the Genomic Sample Prep Kits (Illumina). Blunt ends were created to repair the ends of the ChIP-DNA and the DNA was cleaned with the aid of a PCR purification column (Qiagen) according to the manufacturers suggestion. Again, DNA was purified with the MinElute PCR Purification column (Qiagen). Next, adapters (Sample Prep Kit) were ligated to the ChIP-DNA. The adapter-ligated ChIP-DNA was amplified using Kit-derived oligonucleotides (Sample Prep Kit) with a 22 cycles PCR-run. The size selection of the chip library was attained by separation on a 2%-Agarose gel. The PCR amplified DNA between 200-300 bp was cut out and cleaned with the help of a MinElute gel extraction kit (Qiagen). The size distribution and quantity of the DNA was analyzed through a Bioanalyzer chip (Agilent) before the DNA was used for cluster generation. Single-end sequencing of 36 nucleotides was performed using a Genome Analyzer IIx.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Alignment:Solexa reads were base called using the manufacturer's software SCS 2.5 / RTA 1.5. Subsequently, 3' ligation adapter sequences were identified and removed from the reads. Reads were clipped to 25 bases, and reads shorter than 17 bases were discarded. The remaining reads were mapped against the mouse genome (NCBI37/mm9) allowing up to edit distance 1 per read using a custom read mapping pipeline. Only reads mapping uniquely to the genome were considered. The mapped reads were reduced to non-redundant tag position sets.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
|
| |
|
| Submission date |
Nov 17, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonas Maaskola |
| Organization name |
Max-Delbrueck Centrum Berlin-Buch
|
| Department |
Systems Biology of Gene Regulatory Elements
|
| Lab |
Rajewsky
|
| Street address |
Robert-Roessle Str. 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE33791 |
The SNF2-like helicase HELLS mediates E2F3-dependent transcription and cellular transformation |
|
| Relations |
| SRA |
SRX106016 |
| BioSample |
SAMN00759089 |
| Named Annotation |
GSM835829_ko_hells.bed.gz |
| Named Annotation |
GSM835829_ko_hells_peaks.bed.gz |
| Named Annotation |
GSM835829_ko_hells_summits.bed.gz |
