|
| Status |
Public on Apr 13, 2024 |
| Title |
HCT116 cells (SAE2-kd) - H3K27Ac |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colon carcinoma
chip antibody: Abcam Cat# ab 4729
treatment: Doxycyclin 1ug/mL for 5 days
cell line: shSAE2-stable expression
|
| Treatment protocol |
Cells were treated with 1ug/mL doxycyclin for 5 days to knock down SAE2
|
| Growth protocol |
HCT116 cells stably expressing Tet-On shSAE2 were grown in DMEM at 370C with 5% CO2. Media was supplemented with 10% Tet System Approved FBS, 100 U/ ml-penicillin, and 100 mg/ml streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted and digested using SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. Histone-DNA complexes were isolated with antibody.
Kapa DNA library prep kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequences were aligned to mm9 genome using Novoalign, only unique aligned reads were kept
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using in house R scripts
|
| |
|
| Submission date |
Apr 09, 2021 |
| Last update date |
Apr 13, 2024 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE171804 |
SUMOylation Regulates Super-Enhancers Through Transcription Factor TFAP2C Binding on Chromatin [ChIP-seq] |
| GSE171817 |
SUMOylation Regulates Super-Enhancers Through Transcription Factor TFAP2C Binding on Chromatin |
|
| Relations |
| BioSample |
SAMN18687160 |
| SRA |
SRX10567347 |
