|
| Status |
Public on Jul 31, 2015 |
| Title |
p53 ChIP_MDA-MB-175VII |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-175VII
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-175VII
cell type: breast cancer cell line
p53 mutation status: p53 WT
transfected with: None
chip antibody: Anti-p53, clone DO-1
chip antibody vendor: MABE327
chip antibody cat. #: EMD Millipore
|
| Growth protocol |
All cells were grown in DMEM with 10% FBS, at 20% oxygen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Diagenode Bioruptor.
Sequencing libraries for ChIP-seq were constructd using the NEBNext Ultra kit as per manufacturer's recommended instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
p53 ChIP in MDA-MB-175VII
|
| Data processing |
Raw fastq files were aligned to hg18/ncbi36 using Bowtie, allowing for only uniquely aligned reads to be reported.
bowtie --chunkmbs 512 -m 1 --best <hg18_index> -q <file.fastq> <file.map>
Significant p53 Peaks were called using HOMER, First, HOMER-specifc TagDirectories were generated from bowtie output files (file.map) using the command 'makeTagDirectory <ChIP_TagDirectory> <ChIP_Bowtie_output.map> '
Peaks were then called using command 'findPeaks <tag directory> -style <factor|histone|groseq> -o auto -i <control tag directory>'
p53 Bedgraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto'
For H3K4me3-H3, track views were generated by binning all chIP-seq tags by the position of the tag head into non-contiguous, overlapping 10bp bins for both H3K4me3 and H3. Bin scores were then normalized by the number of millions of reads aligned and H3 scores were subtracted from H3K4me3 scores to normalize for sonication efficiency artifacts
Genome_build: ncbi36/hg18
Supplementary_files_format_and_content: BedGraph files (from HOMER, for visualization in UCSC)
Supplementary_files_format_and_content: BigWig files (for visualization in UCSC)
|
| |
|
| Submission date |
Jul 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Morgan Sammons |
| Organization name |
University of Pennsylvania
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19129 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE59176 |
Prevalent p53 gain-of-function mutants co-opt epigenetic pathways to drive cancer growth |
|
| Relations |
| BioSample |
SAMN02904725 |
| SRA |
SRX647704 |
