|
| Status |
Public on Mar 01, 2023 |
| Title |
4C_insert_mE2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEC-1-B
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human endometrial adenocarcinoma
genotype: mE2
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). HEK-293T 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 and then digested with DpnII and ligated with T4 DNA ligase.
4C libraries were generated by PCR.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
insertion site viewpoint
|
| 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 20, 2020 |
| Last update date |
Mar 01, 2023 |
| Contact name |
yonghu wu |
| E-mail(s) |
yonghuwu88@gmail.com
|
| Phone |
+8615921739862
|
| Organization name |
Shanghai JiaoTong University
|
| Street address |
800# Dongchuan Road
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE147274 |
Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [4C-seq] |
| GSE147286 |
Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus |
|
| Relations |
| BioSample |
SAMN14413143 |
| SRA |
SRX7959336 |
