EXPERIMENT_TITLE: GSM7286681: HiC_CMP_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments. Libraries were generated using the Arima Genomics HiC kit (Arima cat#A101020) Biotinylated fragments were enriched and sheared prior to library preparation which was performed using Accel NGS 2S Plus DNA Library kit (Swift Biosciences)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate their differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - has been shown to bind to regulatory elements in bulk CD34+ HSPCs. However, whether specific combinations of these TFs have distinct roles in regulating hematopoietic differentiation remained unknown. In this study, we mapped the genome-wide binding profiles of these TFs and other chromatin-associated markers in distinct HSPC subsets (HSC, CMP, GMP, MEP). We found that the heptad occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type specific gene expression. Moreover, we observed distinct regulatory elements that were enriched with specific combinations of TFs, such as stem-cell specific elements with ERG, and myeloid and megakaryocyte-erythroid specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. These findings suggest that specific combinations of TFs play critical roles in the regulation of hematopoietic differentiation, and provide a valuable resource for the development of targeted therapies to manipulate specific HSPC subsets. Overall design: HiC
SAMPLE_TITLE: HiC_CMP_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Bone Marrow"}, {"TAG": "tissue", "VALUE": "Bone Marrow"}, {"TAG": "cell type", "VALUE": "CD34+ HSPC"}, {"TAG": "cell subset", "VALUE": "CMP"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: HiC_CMP_rep2
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR24401768", "EXTERNAL_ID": "GSM7286681_r1"}, "EXPERIMENT_REF": {"IDENTIFIERS": {"EXTERNAL_ID": "GSM7286681_r1"}, "@attributes": {"accession": "SRX20189763"}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS17514833", "EXTERNAL_ID": ["SAMN34535691", "GSM7286681"]}, "@attributes": {"member_name": "", "accession": "SRS17514833", "sample_name": "GSM7286681", "sample_title": "HiC_CMP_rep2", "spots": "339254918", "bases": "101776475400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_CMP_rep2_DKDL202005389-1a_HJLWGDSXY_L1_1.fq.gz", "size": "26342381184", "date": "2023-05-02 16:57:51", "md5": "f151130643274cf05caf75e05323a0fc", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_CMP_rep2_DKDL202005389-1a_HJLWGDSXY_L1_2.fq.gz", "size": "26791405858", "date": "2023-05-02 16:58:54", "md5": "218add2afaae1a80e27512b30fbda9ce", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR24401768", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24401768/SRR24401768", "size": "34042942778", "date": "2023-05-02 17:11:32", "md5": "941b0287ce7f3d88d2c0da8faa230e07", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR24401768.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR024/24401/SRR24401768/SRR24401768.lite.1", "size": "25455353838", "date": "2023-05-13 13:19:10", "md5": "53f2b4973de82d2d951a60be95f9855e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "339254918"}}, "Databases": {"Database": {"Table": {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "SEQUENCE"}}}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "101776475400"}}, "@attributes": {"accession": "SRR24401768", "alias": "GSM7286681_r1", "total_spots": "339254918", "total_bases": "101776475400", "size": "34042941551", "load_done": "true", "published": "2023-08-22 01:13:57", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR24401769", "EXTERNAL_ID": "GSM7286681_r2"}, "EXPERIMENT_REF": {"IDENTIFIERS": {"EXTERNAL_ID": "GSM7286681_r1"}, "@attributes": {"accession": "SRX20189763"}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS17514833", "EXTERNAL_ID": ["SAMN34535691", "GSM7286681"]}, "@attributes": {"member_name": "", "accession": "SRS17514833", "sample_name": "GSM7286681", "sample_title": "HiC_CMP_rep2", "spots": "4469248", "bases": "1340774400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_CMP_rep2_DKDL202005389-1a_HJTG3DSXY_L2_1.fq.gz", "size": "360671891", "date": "2023-05-02 13:01:20", "md5": "75daec75228543a40c40a3bb7f869eb3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_CMP_rep2_DKDL202005389-1a_HJTG3DSXY_L2_2.fq.gz", "size": "371918480", "date": "2023-05-02 13:01:14", "md5": "f499fec84990ab74bfbc16eba33499d6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR24401769", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24401769/SRR24401769", "size": "458772866", "date": "2023-05-02 13:01:37", "md5": "edbc06da292280e688f1f8c56fb74a80", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR24401769.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR024/24401/SRR24401769/SRR24401769.lite.1", "size": "335348934", "date": "2023-05-13 11:19:44", "md5": "b833258bbf6e3283a2f56cf16b3481d0", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "4469248"}}, "Databases": {"Database": {"Table": {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "SEQUENCE"}}}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "1340774400"}}, "@attributes": {"accession": "SRR24401769", "alias": "GSM7286681_r2", "total_spots": "4469248", "total_bases": "1340774400", "size": "458771638", "load_done": "true", "published": "2023-08-22 01:13:57", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]