EXPERIMENT_TITLE: GSM5944426: HiC_NCC_INV_rep2; 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_INV_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "CNCC derived from edited H9 hESC"}, {"TAG": "tissue", "VALUE": "CNCC derived from edited H9 hESC"}, {"TAG": "genotype", "VALUE": "Hemizygous inversion"}]
Pool_Member_@attributes_sample_title: HiC_NCC_INV_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_NCC_INV_rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18289615.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR018/18289/SRR18289615/SRR18289615.lite.1", "size": "6473921545", "date": "2022-10-15 11:09:34", "md5": "f18c6467c5f6ac6fb078ee70d262afdb", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18289615", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18289615/SRR18289615", "size": "10368955649", "date": "2022-03-14 15:09:28", "md5": "d2102e96f421d233041f93331da89aa5", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_NCC_INV2_R2.fastq.gz", "size": "7662811878", "date": "2022-03-14 13:00:31", "md5": "7ea13f4d2928e8553dfad60e5c13a36b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_NCC_INV2_R1.fastq.gz", "size": "7484417317", "date": "2022-03-14 12:55:27", "md5": "4251cd988445cb1671acee9f02894257", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]