EXPERIMENT_TITLE: GSM3105137: Hi-C_HepG2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C experiments have been conducted as previously described (Ramírez, Fidel, et al. "High-resolution TADs reveal DNA sequences underlying genome organization in flies." Nature communications 9.1 (2018): 189.), with the following modifications. Nuclei from cell pellets containing about 4 million of cells have been extracted by sonication (Arrigoni, Laura, et al. "Standardizing chromatin research: a simple and universal method for ChIP-seq." Nucleic acids research 44.7 (2015): e67-e67.) using the following parameters: 75W peak power, 2% duty factor, 200 cycles/burst, 180 seconds, using Covaris milliTubes and Covaris E220 sonicator. After nuclei permeabilization, chromatin has been digested overnight at $37ºC using HindIII high fidelity (80 units per million cells; R3104S, NEB). Biotin incorporation has been carried out at 37ºC for one hour in 300 μl volume using these reaction conditions: 50 mM of each nucleotide (dATP, dTTP, dGTP, biotin-14-dCTP, from Life Technologies, 19518-018), 8 U of Klenow (NEB, M0210L). Ligase mix has been added to each sample followed by 4 hours of incubation at room temperature under rotation. After nuclei lysis, protein digestion and overnight de-crosslink, DNA has been precipitated and sonicated to 100-600 bp. Biotinylated DNA has been pulled down as previously described. 100 ng of DNA bound to beads have been used for library preparation using a modification of the NEBNext Ultra DNA library preparation workflow (NEB, E7370). DNA bound to beads has been end-repaired, A-tailed, adaptor-ligated and USER-treated following manufacturer's instruction. After a bead wash, DNA has been eluted from the beads by incubating at 98°C for 10 minutes. Adaptor-ligated DNA has been PCR amplified using 7 PCR cycles. Libraries have been sequenced paired-end, with a read length of 75 bp, on the Illumina NextSeq 500 instrument.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Partially methylated domains, PMDs, are extended regions in the genome exhibiting a reduced average DNA-methylation level. PMDs cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. Here, we present a first comprehensive comparative analysis of PMDs across 171 and 24 WGBS methylomes of human and mouse cells, respectively, providing a deep insight into structural and functional features associated with PMDs. Overall design: Integrative analysis of partially methylated domains across 171 human and 24 mouse WGBS data sets See samples_IDs.xlsx for details on the 171 human and 24 mice datasets
SAMPLE_TITLE: Hi-C_HepG2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HepG2 cell line"}, {"TAG": "cell type", "VALUE": "Hepatocellular carcinoma"}]
Pool_Member_@attributes_sample_title: Hi-C_HepG2
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