EXPERIMENT_TITLE: GSM5944424: HiC_NCC_WT_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_WT_rep2
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_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_NCC_WT_rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18289617.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR018/18289/SRR18289617/SRR18289617.lite.1", "size": "6618980326", "date": "2022-10-20 15:36:50", "md5": "ddc1f2adb38338ce6fff7f0c5f8a0cf5", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18289617", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18289617/SRR18289617", "size": "10608259662", "date": "2022-03-14 16:01:20", "md5": "a2f4fb22d53fb9198119f133c7555c58", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_NCC_WT2_R2.fastq.gz", "size": "7814816399", "date": "2022-03-14 15:12:08", "md5": "e39a5242715ab7df068805ff160fcb17", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_NCC_WT2_R1.fastq.gz", "size": "7650597868", "date": "2022-03-14 14:38:37", "md5": "f9d22d9d09511d432d1eeaba5e7feb16", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]