EXPERIMENT_TITLE: Hi-C of Homo sapiens: atrial cardiomyocyte differentiation at D20 from WTC11 with TBX5in/del rep1
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": "TBX5in/del of ventricular cardiomyocyte (CM) differentiation at D20 rep1"}, {"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": "TBX5_D20_Hom_Rep1_1_R1.fastq.gz", "size": "13258540234", "date": "2024-12-17 19:18:42", "md5": "4c43d8798923dd8c4009a52e339b536a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TBX5_D20_Hom_Rep1_1_R2.fastq.gz", "size": "13451767197", "date": "2024-12-17 19:20:54", "md5": "88c34e8568ce3d46f8173f970dc66062", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TBX5_D20_Hom_Rep1_2_R1.fastq.gz", "size": "18860171120", "date": "2024-12-17 19:19:39", "md5": "bb3645b8cf028505819e263933543b8a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TBX5_D20_Hom_Rep1_2_R2.fastq.gz", "size": "19050729532", "date": "2024-12-17 19:21:26", "md5": "512fff336ff6a03dd6b5aeac9cdc2e0f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TBX5_D20_Hom_Rep1_3_R1.fastq.gz", "size": "18900286091", "date": "2024-12-17 19:19:05", "md5": "80d991e14ddc318c6db86f238d420b10", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TBX5_D20_Hom_Rep1_3_R2.fastq.gz", "size": "19062530932", "date": "2024-12-17 19:20:12", "md5": "0a5746c8e3c0c53ddc0655b62860dcd9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR31752321", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR31752321/SRR31752321", "size": "65867510002", "date": "2024-12-17 19:34:12", "md5": "5bd1d9b65c54943c01cc1bdf23c433cc", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR31752321.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-zq-41/SRR031/31752/SRR31752321/SRR31752321.lite.1", "size": "55736572434", "date": "2024-12-17 21:33:46", "md5": "f16ee174a7c8b32c7b5a9c69275eb9a0", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]