|
| Status |
Public on Jan 04, 2022 |
| Title |
SMC1 Auxin+ rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human colorectal cancer cells
treatment: Auxin
chip antibody: SMC1 (Bethyl lab, Cat# A300-055A)
|
| Treatment protocol |
For inducing auxin-inducible degron system, 500μM 3-indole acetic acid was treated for 6 hours.
|
| Growth protocol |
CTCF degron cells were cultured in RPMI1640 medium supplemented with 10% FBS, 100U/ml Penicillin and 100μg/ml Streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fixed chromatin was sonicated and immunoprecipitated with antibody.
Libraries were prepared using Nextera DNA library preparation kit according to manufacturer's instructions. DNA was amplified using Nextera PCR primers. Libraries were purified using SPRI AMPureXP beads and were paired-end sequenced on Illumina HiSeq2500 platform
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Auxin Inducible Degron cell
|
| Data processing |
sequnced using Illumina HiSeq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the hg19 genome assembly using bwa mem v0.7.17 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD v2.18.23
peaks were called using macs2 v2.2.7.1 with the following setting: -g hs --nomodel -c $INPUT_BAM
normalized enrichment file, bigwig files were generated applying CPM normalization using deeptools v3.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Peak, CPM normalized bigwig
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Jan 05, 2022 |
| Contact name |
Hyoung-Pyo Kim |
| E-mail(s) |
kimhp@yuhs.ac
|
| Organization name |
Yonsei University College of Medicine
|
| Department |
Department of Tropical Medicine
|
| Street address |
Yonsei-ro 50-1
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE179540 |
Genome-wide maps of chromatin state in HCT116 colorectal cancer cell (ChIP-Seq) |
| GSE179545 |
Genome-wide maps of chromatin state in HCT116 colorectal cancer cell |
|
| Relations |
| BioSample |
SAMN20080788 |
| SRA |
SRX11361148 |
