|
| Status |
Public on May 29, 2024 |
| Title |
MB453_UT_K27_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Breast
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
cell line: MDA-MB-453
cell type: Breast Cancer
chip antibody: H3K27ac
treatment: Untreated
|
| Growth protocol |
Cell lines were seeded in DMEM + 10% FBS. After 24h, cells were starved in optimem for 8h then treated with 10ng/ml TWEAK for 48h. TWEAK was replenished after 24h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Diagenode Bioruptor. DNA was sheared to 200-500bp.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using Bowtie2
Peaks were called using MACS2 with subtraction of input signal
bigwig files were generated using deepTools
Assembly: hg38
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Dec 21, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
Yinghui Li |
| E-mail(s) |
liyh@ntu.edu.sg
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Lab |
05n-21
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE231483 |
TWEAK/Fn14 signalling in Breast Cancer |
| GSE251868 |
TWEAK/Fn14 signalling in Breast Cancer (HER2 H3K27ac ChIP-seq) |
|
| Relations |
| BioSample |
SAMN39057709 |
| SRA |
SRX22997286 |
