EXPERIMENT_TITLE: GSM7246730: NPC, INTS10HET2, HiC, biol rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In situ HiC was performed on wildtype and INTS10 heterzygote NPCs (HET2)  using the Arima HiC+ kit (Arima Genomics). Briefly, according to the standard input protocol, 5 million cells were crosslinked then flash-frozen in aliquots of 1 million cells. After quantifying the DNA from 1 million cells, we used two aliquots of cells per condition to meet the amount of DNA (500ng-5ug) required to proceed with the HiC reaction. Digestion and proximity ligation steps were done according to the kit protocol. Proximally ligated DNA underwent quality control checks for ligation efficiency then they were sonicated with the Covaris ME220 sonicator and size selected with DNA purification beads (AMPure XP Beads) to obtain a fragment size distribution of 200-600bp prior to the biotin enrichment step. Finally, libraries were prepared by end repair, dA-tailing, and adaptor ligation using the NEB Next Ultra II DNA Library Prep kit for Illumina, following a protocol tailored for Arima HiC DNA. NEB Next Ultra II DNA Library Prep kit for Illumina, following a protocol tailored for Arima HiC DNA.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Cell fate specification occurs via coordinated transcriptional changes in pluripotent cells, resulting in progressive commitment towards distinct lineages. Lineage-specific transcription factors (TFs), through their intrinsic DNA-binding ability, operate as master orchestrators of early and late developmental processes by turning on select cis-regulatory enhancers and proximal promoter elements. TF binding ultimately drives recruitment of the basal transcriptional machinery that comprises RNA Polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity. Here we show that a set of Integrator subunits (enhancer module) plays a direct role in cell fate specification by promoting epigenetic changes and TF binding at enhancer elements that drive neurogenesis and maintain neuronal cell identity. Depletion of a single Integrator subunit (INTS10) results in loss of molecular and morphological neuronal features, while diverting progenitor cells towards mesenchymal identity. Commissioning of developmental enhancers rely on Integrator's enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. Integrator therefore operates as a functional bridge between enhancers and target promoters and is a driver of early developmental processes, providing new insight into a growing family of neurodevelopmental syndromes. Overall design: Hi-C was done in WT and INTS10heterzyogote NPCs.
SAMPLE_TITLE: NPC, INTS10HET2, HiC, biol rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "NPC"}, {"TAG": "cell line", "VALUE": "NPC"}, {"TAG": "cell type", "VALUE": "neuronal progenitor cell differentated from pluripotent stem cells"}, {"TAG": "genotype", "VALUE": "INTS10HET2"}, {"TAG": "treatment", "VALUE": "No treatment"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: NPC, INTS10HET2, HiC, biol rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: NPC, INTS10HET2, HiC, biol rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR24347802.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-3/SRR024/24347/SRR24347802/SRR24347802.lite.1", "size": "14703946021", "date": "2023-05-06 19:39:27", "md5": "0f7c3fc72cdf5dd6bc5effeebf0e65bd", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR24347802", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24347802/SRR24347802", "size": "18741619197", "date": "2023-04-29 05:41:29", "md5": "7258280cbc3f5a9c57b156a0309942ee", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NPC-INTS10HET2-HiC_R2.fastq.gz", "size": "15861640413", "date": "2023-04-29 05:39:23", "md5": "bda36b302674fbe366fd449de68b6a9d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NPC-INTS10HET2-HiC_R1.fastq.gz", "size": "14704144268", "date": "2023-04-29 05:38:37", "md5": "06df9e60de8212d9c87776414c837e4a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]