EXPERIMENT_TITLE: GSM6454840: HiC_PLN-CD4_HPAP-025_T1D_Rep1T; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C libraries were generated on 1×106 cells using with Arima-HiC+ kit (Arima Genomics) following manufacturer's recommendations. Library was prepared using Accel-NGS @S Plus DNA Library kit (21024 Swift Biosciences), according to the manufacturer's recommendations. Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (66bp+66bp) on NovaSeq 6000 (Illumina).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The spatiotemporal control of gene-expression programs relies on selection and nuclear organization of enhancers. Despite mounting evidence on the formation of multi-enhancer hubs with extensive spatial connectivity, the functional importance of these architectural units remains elusive. Here, we generated a new mouse model and genetically perturbed a genomic locus harboring the Ets1 gene which is hyperconnected in T cells and has strong association with immune-mediated diseases. Although T cell development was intact, competence towards CD4+ T helper 1 specialization was lost in vitro and in vivo after genetic perturbation of the Ets1 locus. Extensive high-resolution molecular mapping of 3D genome organization revealed that the hyperconnectivity of the Ets1 locus controlled the expression level of Ets1 which was required for the Th1-specific genome topology. Our work illustrates the functional relevance of multi-enhancer hub formation in T cells. Overall design: Hi-C
SAMPLE_TITLE: HiC_PLN-CD4_HPAP-025_T1D_Rep1T
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "CD4+ T cells"}, {"TAG": "tissue", "VALUE": "Pancreatic Lymph Node"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "Arima-HiC_HPAP-025_T1D_PLN_CD4_1M_ultraDeep_200885694_S4_R1_001.fastq.gz", "url": "https://sra-pub-src-1.s3.amazonaws.com/SRR21038696/Arima-HiC_HPAP-025_T1D_PLN_CD4_1M_ultraDeep_200885694_S4_R1_001.fastq.gz.1", "size": "188948146291", "date": "2022-08-13 23:34:46", "md5": "2c1e8029219bcebea9c7e250c09c0521", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "Arima-HiC_HPAP-025_T1D_PLN_CD4_1M_ultraDeep_200885694_S4_R2_001.fastq.gz", "url": "https://sra-pub-src-1.s3.amazonaws.com/SRR21038696/Arima-HiC_HPAP-025_T1D_PLN_CD4_1M_ultraDeep_200885694_S4_R2_001.fastq.gz.1", "size": "192733790252", "date": "2022-08-14 00:13:44", "md5": "7bde8535809033d3917838ce182526a7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]