|
Status |
Public on May 10, 2013 |
Title |
FAIRE_Seq_rep2 |
Sample type |
SRA |
|
|
Source name |
Human Mammary Epithelial Cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: Mammary epithelial cells sample type: crosslinked passages: second or third
|
Treatment protocol |
None
|
Growth protocol |
HMEC cells were obtained from Lonza (Lonza, Walkersville, MD) and cultured under recommended conditions.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Nuclei were extracted after the crosslinking step (1% formaldehyde in PBS) of intact cells, followed by re-suspension in SDS lysis buffer before sonication. FAIRE DNA samples were purified by phenol/chloroform extraction. Input DNA was also purified by phenol/chloroform extraction after the crosslinking was reversed. Libraries were prepared according to Illumina's instructions (refer to http://epigenome.usc.edu/services/nextgen/making_libraries.html)
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Basecalls performed using Illumina Casava1.7 software. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to hg19 whole genome using tophat with default parameters. Peaks were called using findPeaks from HOMER (http://biowhat.ucsd.edu/homer), using a triangle-based distribution with a median length of 150bp with an alpha value of 0.01 (99.0% confidence interval) Genome_build: hg19 Supplementary_files_format_and_content: bedGraph files were generated using makeTagDirectory B84and makeUCSCfile from homer with following -o auto -res 1 -fsize 5e7; Peak files were generated using following settings (-alpha 0.01 -subpeaks 0.6) and score represents number of tags found clustered together.
|
|
|
Submission date |
Apr 15, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Suhn K Rhie |
Organization name |
University of Southern California
|
Street address |
1450 Biggy Street
|
City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90089 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE46074 |
Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci |
|
Relations |
BioSample |
SAMN02045903 |
SRA |
SRX265450 |