|
| Status |
Public on Jan 23, 2015 |
| Title |
ZR-75-1 Input [lab: Zhao-DFCI] |
| Sample type |
SRA |
| |
|
| Source name |
Breast Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ZR-75-1
cell line type: luminal-like breast cancer
chip antibody: None
young_id: 20140911_3050
tissue: Breast
cell number: 50 million
|
| Treatment protocol |
None
|
| Growth protocol |
ZR-75-1 cells were grown in RPMI medium supplemented with 10% fetal bovine serum. They were grown to 80-90% confluence by visual inspection and then cross linked with formaldehyde for ten minutes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Aligned to revision hg19 of the human genome using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
Jan 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE65201 |
CDK7-dependent Transcriptional Addition in Basal-like Breast Cancer (ChIP-Seq) |
| GSE69107 |
CDK7-dependent Transcriptional Addiction in Basal-like Breast Cancer |
|
| Relations |
| BioSample |
SAMN03291354 |
| SRA |
SRX850187 |
| Named Annotation |
GSM1589477_20140911_3050.910.rpm.WIG.gz |
