|
Status |
Public on Jan 23, 2015 |
Title |
T47D Input [lab: Zhao-DFCI] |
Sample type |
SRA |
|
|
Source name |
Breast Cancer
|
Organism |
Homo sapiens |
Characteristics |
cell line: T47D cell line type: luminal-like breast cancer chip antibody: None young_id: 20140911_3049 tissue: Breast cell number: 50 million
|
Treatment protocol |
None
|
Growth protocol |
Cells were maintained under typical conditions in RPMI +10% FBS. Cells were grown to 80-90% confluence by visual inspection and cross linked with formaldehyde for 10 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 |
SAMN03291352 |
SRA |
SRX850183 |
Named Annotation |
GSM1589473_20140911_3049.900.rpm.WIG.gz |