|
| Status |
Public on Oct 25, 2012 |
| Title |
FAIRE-seq, THP-1 VD 60min |
| Sample type |
SRA |
| |
|
| Source name |
THP-1 cells, VD, 60min
|
| Organism |
Homo sapiens |
| Characteristics |
cell_line: THP-1
cell_type: monocytic leukemia cells
treatment: 1α,25-dihydroxyvitamin D3
treatment_time: 60 min
|
| Treatment protocol |
Prior to FAIRE sample preparation, cells were grown overnight in phenol red-free medium supplemented with charcoal-stripped fetal bovine serum. Then, cells were treated for the indicated time with vehicle (ethanol, finally 0.1% (v/v)) or 100 nM 1α,25-dihydroxyvitamin D3.
|
| Growth protocol |
Cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard protocol as suggested by the manufacturer for ChIP-seq libraries (also applicable for FAIRE-seq libraries) as utilized at the EMBL Gene Core in Heidelberg, Germany.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
V60.FAIRE.THP1
Open chromatin (enhancers).
|
| Data processing |
Library strategy: FAIRE-Seq
Alignment to hg19 using Bowtie v0.12.5 with the following parameters: -n 1 -k 1 -m 1 -l 28 -t -q --best
Visualization in the Integrative Genomics Viewer via conversions from sam to sorted bam (using samtools) and then to tdf (using igvtools).
Peak discovery using Zinba v1.06 and a common Input control. In Zinba, peak refinement was done and default parameters used except for pWinSize=200 and, as suggested for FAIRE-seq analysis, peakconfidence=0.95.
Genome_build: hg19
Supplementary_files_format_and_content: BED6 format, direct Zinba output.
|
| |
|
| Submission date |
Aug 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sami Heikkinen |
| E-mail(s) |
sami.heikkinen@uef.fi
|
| Organization name |
University of Eastern Finland
|
| Department |
Institute of Biomedicine
|
| Street address |
Yliopistonranta 1E
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE40075 |
Short-term time course of the effects of 1α,25-dihydroxyvitamin D3 treatment on open chromatin regions in THP-1 monocytic leukemia cells |
|
| Relations |
| SRA |
SRX176167 |
| BioSample |
SAMN01112986 |
