|
| Status |
Public on May 10, 2013 |
| Title |
FAIRE_Seq_rep1 |
| 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 |
SAMN02045902 |
| SRA |
SRX265449 |
