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| Status |
Public on Mar 06, 2020 |
| Title |
4C_HEC-1-B_a6_REV-FWD_mut_rep2 |
| Sample type |
SRA |
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| Source name |
HEC-1-B cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HEC-1-B cells
genotype: RF mutation
affected genomic coordinate: chr5:140,404,023-140,404,024 (hg19)
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| 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.
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| 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 for human, mm9 for mouse
Supplementary_files_format_and_content: bedGraph files: the reads per million (RPM) value in 4C-seq experiments.
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| Submission date |
Nov 15, 2019 |
| Last update date |
Mar 07, 2020 |
| Contact name |
Xiao Ge |
| Organization name |
Shanghai JiaoTong University
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| Street address |
No. 800 Dongchuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE138646 |
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection |
| GSE138919 |
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [IV] |
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| Relations |
| BioSample |
SAMN13292315 |
| SRA |
SRX7156664 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4162341_4C_HEC-1-B_a6_REV-FWD_mut_rep2.bedGraph.gz |
74.2 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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