|
| Status |
Public on Oct 01, 2020 |
| Title |
rs9929219_RL_region_bait_SW480 |
| Sample type |
SRA |
| |
|
| Source name |
SW480 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW480
cell type: human colorectal cancer cells
passage: 16-19
|
| Treatment protocol |
The 4C-seq protocol was performed following a protocol(PMID:23411633)
|
| Growth protocol |
The human HCT116 and SW480 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by phenol-chloroform and ethanol precipitated with glycogen as a carrier
4C-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: 4C-seq
The fastq were parsed based on the bait-specific primer sequence and mapped to the reduced hg19 genome using bowtie2 with the default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph with RPM
|
| |
|
| Submission date |
Oct 22, 2018 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Haoyan Chen |
| Organization name |
Renji Hospital
|
| Street address |
145 Shandong Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200001 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE121623 |
Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis |
| GSE121624 |
ZFP90 promotes colorectal carcinogenesis and stemness |
|
| Relations |
| BioSample |
SAMN10268413 |
| SRA |
SRX4913536 |
