EXPERIMENT_TITLE: GSM4983063: ∆CAPH2 1 [Hi-C]; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed as previously described (Rao et al. 2014), with slight modifications as described in (Haarhuis et al. 2017). Replicates were pooled after assessing their similarity. Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes. Overall design: Hi-C was performed in CAPH2 depleted HAP1 cells and compared to previously published wild type HAP1 Hi-C data (GEO accession: GSE95014 - combination of GSM2494290, GSM2494294, and GSM2494298). The hg38_*.hic is generated with a different genomebuild (hg38) and complements the .aca analyses; The hg38_CAPH2.hic file contains the contact matrix of samples GSM4983062 and GSM4983063. The hg38_wildtype.hic incorporates data from the previously published GSMs (GSM2494290,GSM2494294, and GSM2494298).
SAMPLE_TITLE: ∆CAPH2 1 [Hi-C]
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HAP1"}, {"TAG": "cell line", "VALUE": "HAP1"}, {"TAG": "genotype", "VALUE": "delta CAPH2"}]
Pool_Member_@attributes_sample_title: ∆CAPH2 1 [Hi-C]
RUN_SET_RUN_Pool_Member_@attributes_sample_title: ∆CAPH2 1 [Hi-C]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CAPH2_rep2_R1_001.fastq.gz", "size": "12654424787", "date": "2020-12-22 03:02:39", "md5": "de160abcac0da5d87b7a772e182c638c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CAPH2_rep2_R2_001.fastq.gz", "size": "14808447544", "date": "2020-12-22 03:11:56", "md5": "0eb4c612962bc9f3e39627c4d3dcd08b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13281131", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13281131/SRR13281131", "size": "18838286346", "date": "2020-12-22 03:30:47", "md5": "9a441c34079c590efa5597934468d943", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13281131.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/SRR013/13281/SRR13281131/SRR13281131.lite.1", "size": "11728022298", "date": "2022-08-01 03:26:04", "md5": "1effe637be0a87441333c6d562c54d15", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]