|
| Status |
Public on Jun 07, 2023 |
| Title |
shQSER1-1_P53 |
| Sample type |
SRA |
| |
|
| Source name |
Colorectal
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype: QSER1 SH-1
chip antibody: P53(Santa Cruz sc-126)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed according to the previously published protocol (Guo et al.,2020). Briefly, HCT-116 cells were crosslinked with 1% formaldehyde (sigma) for 10 min and quenched with glycine (sangon biotech) for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of ProteinA Agarose (ROCHE) and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq™ Universal SYBR® Green Supermix (Bio-Rad) on CFX96 (Bio-Rad). The ChIP-seq sample preparation kit was used to prepare generate ChIP-seq library.
NEBNext® DNA Library Prep Master Mix Set for Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
For the ChIP-seq data, the reads were aligned to the human genome build HG19 using bowtie2 (v 2.3.5.1) allowing uniquely mapping reads only
Peaks were called with Homer(7) (v4.11) (p < 1e-5) and the density tracks were normalized to reads per million (RPM) based on mapping results.
Genome_build: HG19
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Jul 17, 2021 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Xiaoxu Liu |
| E-mail(s) |
liuxiaoxu1010@126.com
|
| Organization name |
Southeast University
|
| Department |
Institute of Life Sciences
|
| Lab |
the Key Laboratory of Developmental Genes and Human Disease
|
| Street address |
2 Sipailou
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210018 |
| Country |
China |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN20293077 |
| SRA |
SRX11489337 |
