|
| Status |
Public on Mar 11, 2020 |
| Title |
4C_HEC-1-B_a12_WT_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
4C_HEC-1-B_a12_WT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEC-1-B
cell type: human endometrial adenocarcinoma
genotype/variation: wildtype
restriction enzyme: DpnII
|
| Growth protocol |
Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). Human K562 cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After cross-linking with 2% formaldehyde, cells were lysed twice with cold lysis buffer, digested with DpnII, ligated with T4 DNA ligase.
4C libraries were generated by PCR.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: 4C-seq
Sequenced reads were trimmed for adaptor sequence and the bait sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files: the reads per million (RPM) value in 4C-seq experiments.
|
| |
|
| Submission date |
Mar 10, 2020 |
| Last update date |
Mar 11, 2020 |
| Contact name |
Xiao Ge |
| Organization name |
Shanghai JiaoTong University
|
| Street address |
No. 800 Dongchuan Road
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE138919 |
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [IV] |
|
| Relations |
| BioSample |
SAMN14342647 |
| SRA |
SRX7886255 |
