|
| Status |
Public on Dec 18, 2018 |
| Title |
THP-1 24h after EtOH treatment, 3rd replicate CEBPA |
| Sample type |
SRA |
| |
|
| Source name |
Culture
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
treatment: EtOH
time point: 24h
chip antibody: anti-CEBPA (Diagenode, catalog number: C15410225)
|
| Treatment protocol |
Cells were treated with either 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, ChIPmentation was performed.
The library was created using NEBNext Ultra II DNA Library Prep Kit for Illumina and the samples were barcoded using Nextera sequencing primers. The pooled libraries were sequenced on an Illumina HiSeq2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CEBPA EtOH 24 h N3
ChIPmentation
processed data file: THP1_CEBPA_merged_ET.txt
|
| Data processing |
Alignment to hg19 using Bowtie v1.1 Parameters -n 1 -k 1 -m 1 -l 32 -t -q best
Peak calling using MACS2, parameters bw 150 min peak 3 max peak 50
EtOH treated merged and considered as a unique file.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files
Supplementary_files_format_and_content: THP1_CEBPA_2h_EtOH.tdf
|
| |
|
| Submission date |
Dec 18, 2018 |
| Last update date |
Dec 19, 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) |
| GSE119556 |
The pioneer factor CEBPA modulates vitamin D signaling |
| GSE124032 |
Effects of vitamin D on CEBPA binding in THP-1 cells |
|
| Relations |
| BioSample |
SAMN10610949 |
| SRA |
SRX5157164 |
