EXPERIMENT_TITLE: GSM8249253: HN_HiC_051_human_invitroTh2_nostim_donor1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: A detailed protocol to generate HiC libraries can be obtained at PMID:25497547 and PMID:26499245
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The type 2 cytokines, interleukin (IL)-4, IL-5 and IL-13 reside within a multi-gene cluster in mammals. These cytokines represent the hallmark of type 2 immune responses controlling parasites and promoting tissue repair, as well as causing allergic diseases. Both innate and adaptive lymphocytes secrete type 2 cytokines with discordant production spectra. We took a holistic structural and functional view of the type 2 cytokine locus before and after activation, comparing innate (ILC2) and adaptive (Th2) lymphocytes to understand mechanisms underlying their distinctive programs. Rapid induction of IL-5 dominates in ILC2, whereas IL-4 does so in Th2 cells. Using high-resolution chromatin conformation capture we found that global cellular chromatin architecture remained constant, whereas the type 2 cytokine locus rapidly remodeled. In ILC2, Il13 and Il5 loci were aligned in proximity whereas Il4 locus was insulated. In Th2 cells, Il4 and Il13 positioned in proximity while the Il5 locus remained distal. Select REs were individually deleted in mice to confirm cell-type specific and activation-dependent roles in type 2 responses in vivo. Thus, contrary to the premise that chromatin architecture plays a minimal role in steady-state gene induction, signal-dependent remodeling of 3D configuration underlies the discordant cytokine outputs in ILC2s versus Th2 cells. Overall design: HiC for mouse ILC2s, mouse Th2 and human Th2 cells.
SAMPLE_TITLE: HN_HiC_051_human_invitroTh2_nostim_donor1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "blood"}, {"TAG": "tissue", "VALUE": "blood"}, {"TAG": "cell type", "VALUE": "Th2"}, {"TAG": "genotype", "VALUE": "donor1"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: HN_HiC_051_human_invitroTh2_nostim_donor1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HN_HiC_051_human_invitroTh2_nostim_donor1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HN_HiC_051_human_invitroTh2_nostim_donor1.fq.r1.gz", "size": "35397331677", "date": "2024-05-03 16:05:57", "md5": "396d2cb4b3f6c2fd86dea1c48184a1ec", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HN_HiC_051_human_invitroTh2_nostim_donor1.fq.r2.gz", "size": "35060704475", "date": "2024-05-03 16:03:50", "md5": "035d04c5843bdc583e201a9a4e0d8924", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR28886834", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR28886834/SRR28886834", "size": "37154970462", "date": "2024-05-03 16:16:06", "md5": "e3c2800a2659254e10140831e325654f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR28886834.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR028/28886/SRR28886834/SRR28886834.lite.1", "size": "29587376310", "date": "2024-05-03 16:26:06", "md5": "65089e380860e5e8811005dc5bae7e2b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]