EXPERIMENT_TITLE: GSM5944423: HiC_NCC_WT_rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Nuclear extraction-see accompanying manuscript as per Belaghzal, H., Dekker, J., and Gibcus, J.H. (2017). Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods 123, 56–65.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Examination of the chromatin state and chromatin architecture of a region on human chromosome 7 and the orthologous region on mouse chromosome 6. Overall design: ChIP-seq for multiple histone marks, RNA-seq, HiC and 4C-seq in a cell culture model of human cranial neural crest and mouse, both wild type and CRISPR/Cas9 edited with HiC of primary human tissue for comparison of chromatin architecture. Human raw data is being submitted to dbGaP [CS17_HiC]
SAMPLE_TITLE: HiC_NCC_WT_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "H9-derived CNCC"}, {"TAG": "tissue", "VALUE": "H9-derived CNCC"}, {"TAG": "genotype", "VALUE": "WT"}]
Pool_Member_@attributes_sample_title: HiC_NCC_WT_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_NCC_WT_rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18289618.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR018/18289/SRR18289618/SRR18289618.lite.1", "size": "8218677560", "date": "2022-10-14 13:19:00", "md5": "45be24e7f46661e751bf18de444d7fda", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18289618", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18289618/SRR18289618", "size": "13273180160", "date": "2022-03-24 05:13:53", "md5": "e69b7d40847d96047e8d2d241bbd7223", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_NCC_WT1_R2.fastq.gz", "size": "9751312415", "date": "2022-03-24 05:04:03", "md5": "a4030f50d1327249d991596ba1ab37cc", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_NCC_WT1_R1.fastq.gz", "size": "9533836139", "date": "2022-03-24 05:06:44", "md5": "3aed4e20b033a49ab0530a93d4954b03", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]