EXPERIMENT_TITLE: GSM8067794: Hi-C GM13976 rep6; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were crosslinked in 1% v/v formaldehyde for ten minutes and quenched by adding 2.5 M glycine to a final concentration of 0.2 M for 5 min. Cells were pelleted by centrifugation at 300 G for 5 min at 4 °C and then washed with cold PBS. Cells were lysed with lysis buffer containing 10 mM Tri-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630 and protease inhibitors for 15 min on ice. Cells were centrifuged at 300 G and washed in that same buffer, and then resuspended in 50 µl 0.5% SDS for 5 min at 62 °C. Afterward, 145 µl of water and 25 µL of Trition X-100 were added and incubated at 37 °C for 15 min. Chromatin was digested overnight in MboI, MseI, or NlaIII in the corresponding buffer. Fragment overhangs were repaired and biotinylated using equal amounts of biotin-14-dATP, dCTP, dGTP, and dTTP in the presence of 40 units of DNA Polymerase I, Large (Klenow) Fragment at 37 °C for 1 h. Chromatin was ligated in 1x T4 DNA ligase buffer, Triton X-100, 0.12 mg BSA, and 2000 units T4 DNA ligase at room temperature for four hours. Proteins were digested, and chromatin decrosslinked in 0.72 mg/ml proteinase k, 1% SDS, and 0.5 M NaCl for 30 min at 55 °C, followed by 68 °C overnight. Libraries were sequenced and then processed using Illumina HiSeq 4000 software and JuicerTools v1.14.08. As per Harris, Hannah L., et al. "Chromatin alternates between A and B compartments at kilobase scale for subgenic organization." Nature Communications 14.1 (2023): 3303.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The co-visualization of chromatin conformation with 1D 'omics data is key to the multi-omics driven data analysis of 3D genome organization. Chromatin contact maps are often shown as 2D heatmaps and visually compared to 1D genomic data by simple juxtaposition. While common, this strategy is imprecise, placing the onus on the reader to align features with each other. To remedy this, we developed HiCrayon, an interactive tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. This visualization method integrates data from genomic assays directly into the chromatin contact map by coloring interactions according to 1D signal. HiCrayon is implemented using R shiny and python to create a graphical user interface (GUI) application, available in both web or containerized format to promote accessibility. HiCrayon is implemented in R, and includes a graphical user interface (GUI), as well as a slimmed-down web-based version that lets users quickly produce publication-ready images. We demonstrate the utility of HiCrayon in visualizing the effectiveness of compartment calling and the relationship between ChIP-seq and various features of chromatin organization. We also demonstrate the improved visualization of other 3D genomic phenomena, such as differences between loops associated with CTCF/cohesin vs. those associated with H3K27ac. We then demonstrate HiCrayon's visualization of organizational changes that occur during differentiation and use HiCrayon to detect compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct 3rd chromatin compartment. Overall, we demonstrate the utility of co-visualizing 2D chromatin conformation with 1D genomic signals within the same matrix to reveal fundamental aspects of genome organization. Overall design: Hi-C samples from 8 cell lines in LCL, with replicates ranging from 3 to 34. The following shows cell line with replicate number; AK1: 9, GM12878: 34 (re-analyzed; raw files not uploaded. Only processed combination), GM12891: 4, GM12892: 3, GM13976: 16, GM13977: 16, GM18526: 20, GM19239: 24 Please note that the GM12878.hic was generated by re-analyzing the 'GSM1551550-GSM1551578' samples (in GSE63525) and the re-analyzed sample details are provided in the 're-analyzed_sample_accns.txt'
SAMPLE_TITLE: Hi-C GM13976 rep6
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Lymphoblastoid"}, {"TAG": "tissue", "VALUE": "Lymphoblastoid"}, {"TAG": "cell line", "VALUE": "GM13976"}, {"TAG": "cell type", "VALUE": "cell line"}, {"TAG": "genotype", "VALUE": "MboI restriction enzyme digested"}, {"TAG": "treatment", "VALUE": "No treatment"}, {"TAG": "biomaterial provider", "VALUE": "http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM13976"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Hi-C GM13976 rep6
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C GM13976 rep6
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