|
| Status |
Public on Dec 18, 2018 |
| Title |
THP-1 2h after 1,25D treatment, 3rd replicate H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
treatment protocol: 2h with 1,25(OH)2D3
chip antibody: H3K4me3
|
| Treatment protocol |
Cells were treated with 100 nM of 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% ethanol).
|
| Growth protocol |
THP-1 cells were grown in RPMI 1640 medium, supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were grown in culture as mentioned above, after which they were crosslinked with formaldehyde, lysed and the DNA was extracted. Then, ChIP was performed using antibody against H3K4me3 (Millipore, cat.# 07-473, lot# 2557645).
ChIP DNA was sent to EMBL and the library was prepared there according to their protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H3K4me3 2 VD N3
|
| Data processing |
Alignment to hg19 using Bowtie v1.1 Parameters -n 1 -k 1 -m 1 -l 32 -t -q best
Peak calling using Zinba v 2.02 Parameters -f 200
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tdf, bed
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Dec 18, 2018 |
| 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 (2) |
| GSE119555 |
Effects of vitamin D on histone modification H3K4me3 in THP-1 cells |
| GSE119556 |
The pioneer factor CEBPA modulates vitamin D signaling |
|
| Relations |
| BioSample |
SAMN09981714 |
| SRA |
SRX4645752 |
