|
| Status |
Public on Dec 20, 2023 |
| Title |
HGC27, RUNX3KO, H3K27ac, ChIP, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HGC27
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HGC27
cell type: RUNX3 knock-out
chip antibody: H3K27ac
|
| Growth protocol |
MEM, 10% fetal bovine serum, 1x penicillin/streptmycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Picoruptor (Diagenode).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. 10 ng of DNA was used as starting material for Input and ChIP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Tapestation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq.
ChIP-seq experiment were aligned to UCSC human genome (hg19) using bowtie 1.0.1.
Duplicated reads were removed with Picard tools 2.3.0.
bigWig files were generated using HOMER 4.11.1.
Peaks were called using HOMER 4.11.1 findPeaks.
Assembly: hg19
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Dec 18, 2023 |
| Last update date |
Dec 20, 2023 |
| Contact name |
Masaki Fukuyo |
| E-mail(s) |
fukuyo@chiba-u.jp
|
| Organization name |
Chiba University
|
| Department |
Department of Molecular Oncology
|
| Street address |
1-8-1 Inohana, Chuo-ku
|
| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18460 |
| Series (2) |
| GSE250479 |
Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer (ChIP-seq) |
| GSE250481 |
Aberrant upregulation of RUNX3 activates developmental genes to drive metastasis in gastric cancer. |
|
| Relations |
| BioSample |
SAMN38914987 |
| SRA |
SRX22955443 |
