|
| Status |
Public on Mar 01, 2021 |
| Title |
SW480M P65 ChIP-Seq rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: cat no:33-9900, lot no: QJ216251, mouse monoclonal, Invitrogen
cell line: SW480
transfection: stably transfected with empty vector
|
| Treatment protocol |
All Cells were treated with TNFα (30ng/ml, 11088939001, Roche, lot no: 25885600) for 30 minutes before ChIP experiment.
|
| Growth protocol |
Cells were cultured in Dulbecco's modified Eagle’s medium (Sigma-Aldrich) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (P/S) and 1% blasticidine (Sigma Aldrich).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with DSG (20593, lot TF263080, Thermo Scientific) for 45 min and then incubated with formaldehyde (1%) for 10 minutes. Nuclear chormatin fractions were separted and immunoprecipitated with P65 anitboides.
The libraries of ChIP DNA were prepared by using the kit NEB Next Ultra II DNA Library Prep Kit for Illumina following user instrcutions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
ChIP-Seq reads were mapped to the human reference genome assembly hg38(GRCh38) using STAR and reads which assigned to multiple locations were discarded. P65-binding sites were identified by HOMER applying a false dis-covery rate (FDR) less than 0.001 and four-fold enrichment over control (Input) cut-off. Peaks present in at least 2 out of 3 replicates were considered for downstream analysis. De novo motif analysis of identified binding sites was performormed using HOMER.
Genome_build: hg38(GRCh38)
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Nov 04, 2020 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Rajitha Indukuri |
| E-mail(s) |
[email protected]
|
| Phone |
0760285999
|
| Organization name |
Scilifelab
|
| Street address |
Tomtebodavägen 23a, Solna
|
| City |
Stockholm |
| State/province |
Sweden |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE160856 |
ERbeta influencing p65 cistromes in colon cancer cells |
|
| Relations |
| BioSample |
SAMN16666633 |
| SRA |
SRX9434359 |
