|
| Status |
Public on May 04, 2023 |
| Title |
HuhWT_UN_INP |
| Sample type |
SRA |
| |
|
| Source name |
Huh7.5
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7.5
cell type: human hepatocellular carcinoma cells
chip antibody: none
|
| Treatment protocol |
Cells were seeded in full cell culture medium, which was replaced the next day with starving medium containing 1% FBS for 8h before starting the treatment
IFNα (1000 U/ml, IF007, MERCK) or IFNγ (10 ng/ml, IF002, MERCK) was added for indicated time points
|
| Growth protocol |
Huh7.5 WT cell line was maintained in DMEM complete medium supplemented with 10% fetal bovine serum (FBS), 1% MEM NEAA and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was carried out as previously described (Piaszyk-Borychowska et al. 2012)
ChIP-seq libraries were prepared using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (E6240, NEB) and NEBNext® Multiplex Oligos for Illumina®, according to the manufacturer's protocol. Libraries were validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
unstimulated Huh7.5 wild type cells, input
|
| Data processing |
After quality assessment of raw reads with FastQC, ChIPseq data was analyzed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline v3 (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters (ENCODE Project Consortium, 2012)
regionPeak files were generated using SPP with default settings, FDR threshold set to 0.01
Assembly: hg38
Supplementary files format and content: regionPeak (except for input sample). High-confidence peaks obtained after IDR evaluation between biological replicates (optimal output peak set; https://www.encodeproject.org/data-standards/terms/)
|
| |
|
| Submission date |
Jan 11, 2023 |
| Last update date |
May 04, 2023 |
| Contact name |
Hans A.R. Bluyssen |
| E-mail(s) |
[email protected]
|
| Phone |
+48 061 8295832
|
| Organization name |
Adam Mickiewicz University
|
| Department |
Laboratory of Human Molecular Genetics
|
| Street address |
Uniwersytetu Poznańskiego 6
|
| City |
Poznan |
| ZIP/Postal code |
61-614 |
| Country |
Poland |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE222667 |
Time-dependent recruitment of GAF, ISGF3 and IRF1 complexes to GAS, ISRE and composite genes shapes IFNa and IFNg activated transcriptional responses and explains functional overlap [CHIP-seq] |
| GSE222668 |
Time-dependent recruitment of GAF, ISGF3 and IRF1 complexes to GAS, ISRE and composite genes shapes IFNa and IFNg activated transcriptional responses and explains functional overlap |
|
| Relations |
| BioSample |
SAMN32679204 |
| SRA |
SRX19004965 |
