|
| Status |
Public on Jan 01, 2016 |
| Title |
FAIRE-seq at 0 h, replicate A |
| Sample type |
SRA |
| |
|
| Source name |
monocytic cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
treatment: untreated
treatment time: 0 h
|
| Treatment protocol |
cells were either treated with 100 nM of the natural VDR ligand 1,25-dihydroxyvitamin D3 (Sigma-Aldrich) or unstimulated
|
| Growth protocol |
THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
proteins were crosslinked with formaldehyde to DNA, then open chromatin fragments were isolated by phenol-chloroform extraction
Standard protocol as suggested by the manufacturer for ChIP-seq libraries as utilized at the EMBL Gene Core in Heidelberg, Germany
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
crosslinked before phenol-chloroform extraction
|
| Data processing |
Alignment to hg19 using Bowtie v1.0 with the following parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Peak discovery using MACS2 with parameters: -m 5 50 –bw 150
Visualization as tdf in Integrative Genomics Viewer via conversion from sam to sorted bam (using samtools) and then to tdf (using igvtools)
Genome_build: hg19
Supplementary_files_format_and_content: TDF generated by IGVtools
|
| |
|
| Submission date |
May 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Carsten Carlberg |
| E-mail(s) |
carsten.carlberg@uef.fi
|
| Organization name |
University of Eastern Finland
|
| Department |
Institute of Biomedicine
|
| Street address |
Yliopistonranta 1D
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE69297 |
FAIRE-seq 1,25(OH)2D3 time course in THP-1 cells |
| GSE69303 |
1,25(OH)2D3 time course in THP-1 cells |
|
| Relations |
| BioSample |
SAMN03737923 |
| SRA |
SRX1041079 |
