|
| Status |
Public on Oct 26, 2016 |
| Title |
MCF10A FAIRE-seq input |
| Sample type |
SRA |
| |
|
| Source name |
MCF10A FAIRE-seq input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
cell type: Human breast cell line
|
| Growth protocol |
The immortalized human normal breast cell line MCF10A (ATCC # CRL-10317) was maintained in DMEM/F12 with 5% horse serum, 100units/ml penicillin, 0.1mg/ml streptomycin, 0.5ug/ml hydrocortisone, 100ng/ml cholera toxin, 10ug/ml insulin, and 20ng/ml epidermal growth factor (EGF).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For FAIRE-seq, 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.
FAIRE-seq: Libraries were prepared according to Illumina's instructions (http://epigenome.usc.edu/services/nextgen/making_libraries.html)
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FAIRE-seq reads were aligned to hg19 genome assembly using bwa.
For FAIRE-seq, Sole-Search (TF parameter, alpha value: 0.001, fdr: 0.001) was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: For FAIRE-seq, tab-delimited text files include location of peaks
|
| |
|
| Submission date |
May 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Suhn K Rhie |
| Organization name |
University of Southern California
|
| Department |
Biochemistry and Molecular Medicine
|
| Lab |
Rhie Lab
|
| Street address |
1450 Biggy Street NRT 3504
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE78913 |
Tracing Enhancer Networks using Epigenetic Traits (TENET) |
|
| Relations |
| BioSample |
SAMN05170550 |
| SRA |
SRX1795460 |
