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Status |
Public on Mar 06, 2020 |
Title |
4C_p0-cortex_HS5-1_HS5-1bdel_rep1 |
Sample type |
SRA |
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Source name |
P0 cortex
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Organism |
Mus musculus |
Characteristics |
cell type: P0 cortex genotype: HS5-1b deletion affected genomic coordinate: chr18:37,377,774-37,378,246 (mm9)
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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 |
GPL17021 |
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 |
SAMN13292252 |
SRA |
SRX7156757 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4162446_4C_p0-cortex_HS5-1_HS5-1bdel_rep1.bedGraph.gz |
841.7 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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