|
| Status |
Public on Jul 18, 2017 |
| Title |
THP-1, VDR 24 h EtOH replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
human monocytic cell line THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: monocytic cell line THP-1
treatment: EtOH
time: 24 h
chip antibody: VDR (Cell Signaling Technologies CST 12550)
|
| Treatment protocol |
Treated with EtOH or 24 h 100 nM 1,25(OH)2D3
|
| 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 VDR-bound fragments were pulled down by chromatin immunoprecipitation
ChIP-seq library was prepared from 5-10 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) per manufacturer's protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against VDR
|
| Data processing |
Alignment to hg19 using Bowtie v1.0 parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Peak discovery using MACS2 parameters: -m 5 50 –bw 150
Genome_build: hg19
Supplementary_files_format_and_content: tdf
|
| |
|
| Submission date |
Nov 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Carsten Carlberg |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Eastern Finland
|
| Department |
Institute of Biomedicine
|
| Street address |
Yliopistonranta 1D
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE89431 |
VDR ChIP-seq in human monocytic THP-1 cells |
|
| Relations |
| BioSample |
SAMN05967533 |
| SRA |
SRX2319760 |
