|
Status |
Public on Oct 01, 2020 |
Title |
rs9929218_RR_region_bait_HCT116 |
Sample type |
SRA |
|
|
Source name |
HCT116 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HCT116 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 |
SAMN10268416 |
SRA |
SRX4913533 |