|
| Status |
Public on May 27, 2014 |
| Title |
NS_input_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
MCF7_unstimulated_input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer cells
stimulated with: none (unstimluated (NS) control)
chip antibody: none
|
| Treatment protocol |
Cells were either stimulated with 5μM Nutlin-3a (in case of p53-WT cells) for 24h or left untreated.
|
| Growth protocol |
p53-WT MCF-7 cells were seeded at a density of 5 million cells per 15 cm dish and grown ON at 37°C to a confluency of 80-90%.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP samples were prepared following the Magna ChIP-seqTM preparation kit
5-10 ng of precipitated DNA was used to perform library preparation according to the Illumina TruSeqTM DNA Sample preparation guide. In brief, the immunoprecipitated DNA was end-repaired, A-tailed, and ligated to diluted sequencing adapters (dilution of 1/100). After PCR amplification with 15-18 cycles and gel size selection of 200–300bp fragments, the libraries were sequenced using the HiSeq 2000 (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-seq with input DNA on Non stimulated cells
|
| Data processing |
An initial filtering was performed to remove reads containing residual adapter sequences (fastx_clipper, version 0.013, option –M15).
Next, a quality report was generated using the FastQC software (version 0.9) checking the reads for PHRED quality (> 20), read length (> 20) and primer- contamination.
Filtered reads were mapped to the human reference genome hg19 (UCSC) using bowtie (v2.0.0-beta3) with the addition of parameter –local, allowing for further soft clipping of the reads.
An extra filtering on the mapping score ensured that only reads with a minimum score of 4 were kept for further analysis.
Peak calling was performed using MACS (version 1.4.2) with a threshold for p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: output bed files from MACS and merged nutlin stimulated wig file
|
| |
|
| Submission date |
May 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
rekins.janky@med.kuleuven.be
|
| Organization name |
KU Leuven
|
| Department |
Department of Human Genetics
|
| Lab |
Laboratory of Computational Biology
|
| Street address |
Herestraat 49 box 602
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE47041 |
Discovery of the p53 targetome in MCF7 cells from ChIP-Seq data |
| GSE47043 |
Discovery of the p53 targetome in MCF7 cells from RNA-seq and ChIP-seq data |
|
| Relations |
| BioSample |
SAMN02146487 |
| SRA |
SRX281475 |
