|
| Status |
Public on Nov 10, 2021 |
| Title |
HCT116: Human colorectal carcinoma cells-input DNA |
| Sample type |
SRA |
| |
|
| Source name |
Human colorectal carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: Human colorectal carcinoma cells
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) assays were performed using a ChIP assay kit (Millipore, Temecula, USA) according to the manufacturer’s instructions. Briefly, cells were fixed with formaldehyde and homogenized. Nuclei were pelleted, and DNA was sheared by sonication and immunoprecipitated with anti-RUNX2 antibody or negative control immunoglobulin G using protein A/G beads. DNA was released from immunoprecipitate complexes using proteinase K and purified. Chromatin was sheered by 8 sonication cycles to generate DNA fragments with an average size of 200 bp for ChIP-seq analysis and 4 sonication cycles to generate DNA fragments with an average size of 600 bp for ChIP-qPCR.
For high-throughput sequencing, 10-20 ng DNA was used to make the ChIP-seq library according to the instructions from Illumina’s ChIP-seq Sample Prep kit. The ChIP-seq library was loaded on Illumina’s cluster station and sequenced with Illumina Genome Analyzer IIx.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Sequenced reads were aligned to the human genome, and reads with more than two aligned positions were removed. The remaining tags were further filtered by quality score and redundancy. Only nonredundant reads that passed the quality score were retained for downstream analysis. ChIP-seq tags and whole genome sequencing tags were then analyzed using MACS to identify the peaks based on p < 0.005
The remaining tags were further filtered by quality score and redundancy.
Only nonredundant reads that passed the quality score were retained for downstream analysis.
ChIP-seq tags and whole genome sequencing tags were then analyzed using MACS to identify the peaks based on p < 0.005
Genome_build: mm9
|
| |
|
| Submission date |
Jul 02, 2020 |
| Last update date |
Nov 10, 2021 |
| Contact name |
chen Wang |
| E-mail(s) |
chenwangnju@outlook.com
|
| Organization name |
Nanjing University
|
| Street address |
xianlin street num 163
|
| City |
Nanjing |
| ZIP/Postal code |
210037 |
| Country |
China |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE153682 |
CBFβ promotes colorectal tumor growth and metastasis in a RUNX2-dependent manner (ChIP-seq) |
| GSE154876 |
CBFβ promotes colorectal tumor growth and metastasis in a RUNX2-dependent manner |
|
| Relations |
| BioSample |
SAMN15423676 |
| SRA |
SRX8655728 |
