EXPERIMENT_TITLE: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation from WTC11 at D11 rep2
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Dosage-sensitive transcription factors (TFs) underlie altered gene regulation in congenital heart disease (CHD), and cell-type specific gene regulation is linked to the reorganization of 3D chromatin during cellular differentiation. Here, we show dose-dependent regulation of chromatin organization by the congenital heart disease (CHD)-linked, lineage-restricted TF TBX5 in human cardiomyocyte differentiation. Genome organization, including compartments, topologically associated domains, and chromatin loops, are sensitive to reduced TBX5 dosage in a human model of CHD, with variations in response across individual cells. Regions normally bound by TBX5 were especially sensitive, while co-occupancy with CTCF partially protected TBX5-bound TAD boundaries and loop anchors. These results highlight the importance of lineage-restricted TF dosage in cell-type specific 3D chromatin dynamics, suggesting a new mechanism for TF-dependent disease.
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "D11 of atrial cardiomyocyte (CM) differentiation rep2"}, {"TAG": "age", "VALUE": "NA"}, {"TAG": "biomaterial_provider", "VALUE": "NA"}, {"TAG": "collection_date", "VALUE": "NA"}, {"TAG": "geo_loc_name", "VALUE": "NA"}, {"TAG": "sex", "VALUE": "not applicable"}, {"TAG": "tissue", "VALUE": "NA"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Atrial_D11_Rep2_1_R1.fastq.gz", "size": "23691251557", "date": "2024-12-17 20:13:57", "md5": "6b2e901ec17203021059af9e31c01d35", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Atrial_D11_Rep2_1_R2.fastq.gz", "size": "25005052477", "date": "2024-12-17 20:15:47", "md5": "eb27e68a1f24ab6813ae3bdbcb1d583e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Atrial_D11_Rep2_2_R1.fastq.gz", "size": "14622309116", "date": "2024-12-17 20:14:39", "md5": "b44f2bec9a4d8cceded61fe76f01deda", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Atrial_D11_Rep2_2_R2.fastq.gz", "size": "15302869707", "date": "2024-12-17 20:11:39", "md5": "4fadc9f02827b930f546dc35c4e7dda9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Atrial_D11_Rep2_3_R1.fastq.gz", "size": "15132380634", "date": "2024-12-17 20:12:11", "md5": "fef201724e8cd1388a42d8a1290a2576", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Atrial_D11_Rep2_3_R2.fastq.gz", "size": "15910997911", "date": "2024-12-17 20:12:47", "md5": "26190a28a5f242b0fdfe29c796484e4e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR31752326", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR31752326/SRR31752326", "size": "70999988731", "date": "2024-12-17 20:33:06", "md5": "9e6b6f6f85ff7078066fe42ef6f2aa54", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR31752326.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-zq-41/SRR031/31752/SRR31752326/SRR31752326.lite.1", "size": "53394212235", "date": "2024-12-17 22:21:33", "md5": "1aa19bb686bf21cc538633ea3775c45f", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]