EXPERIMENT_TITLE: Hi-C of hiNSCs
STUDY_DESCRIPTOR_STUDY_ABSTRACT: How 3D genome organization regulates cell fate transition remains poorly understood at present. By multiomics analyses integrating the Hi-C data, PTF1A and CTCF DNA-binding profiles, H3K27ac modification, and gene expression, we demonstrate that 3D genome reorganization as a driving force instrumental for cellular transcription program changes and cell fate transitions, and highlight an essential role for PTF1A in orchestrating multiscale 3D genome remodeling during cell reprogramming.
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "PTF1A induced NSC derived human fibroblasts"}, {"TAG": "age", "VALUE": "4"}, {"TAG": "biomaterial_provider", "VALUE": "Zhongshan Ophthalmic Center"}, {"TAG": "collection_date", "VALUE": "2021"}, {"TAG": "geo_loc_name", "VALUE": "China"}, {"TAG": "sex", "VALUE": "male"}, {"TAG": "tissue", "VALUE": "foreskin"}, {"TAG": "ID", "VALUE": "5"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC-iNSC-1_Q021-H09-1_good_1.fq.gz", "size": "42332115627", "date": "2023-08-07 01:13:19", "md5": "39cf568a879f66ab83733ea4156921e8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC-iNSC-1_Q021-H09-1_good_2.fq.gz", "size": "44835069730", "date": "2023-08-07 01:11:17", "md5": "4436d38c339996988267e69dc58b0ef3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR25544871", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25544871/SRR25544871", "size": "62037347999", "date": "2023-08-07 01:17:59", "md5": "edc860aa9cca178b02234b26a9c3cb8d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR25544871.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR025/25544/SRR25544871/SRR25544871.lite.1", "size": "48002303375", "date": "2023-08-12 04:58:03", "md5": "78cd0b036a0525d37f7befb704917504", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]