EXPERIMENT_TITLE: GSM7462252: HiC in ZNF274KO 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The Hi-C libraries were prepared using Arima-HiC (Arima Genomics), following the manufacturer's protocol. For all samples, 5 million cells were fixed in 1% methanol-free formaldehyde solution for 10min at RT and the reaction was quenched for 5min with glycine to a final concentration of 125 mM. UMI-4C experiments were performed as described previously (Schwartzman et al. 2016). Briefly, 5 million cells were fixed in 1% methanol-free formaldehyde solution for 10min at RT and the reaction was quenched for 5min with glycine to a final concentration of 125 mM. Cells were lysed in ice-cold Lysis Buffer (10mM Tris HCl pH 8,10mM NaCl, 0.2% NP-40), chromatin was digested with 800U DpnII (NEB), and digested ends were marked with biotin UMI- 4C (https://pubmed.ncbi.nlm.nih.gov/27376768/) is a 3D technique involving  primers and biotinilation/ligation to infer the contacts points of regions of interest. It's very similar to a 4C with the addition of UMI for deduplication.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Epigenetic mechanisms influencing chromatin architecture are key to the spatio-temporal control of transcription. Here we identify ZNF274 as a new regulator of chromosome compartmentalization that silences lineage-specific gene clusters. ZNF274 is a SCAN-bearing member of the Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs). Ablation of ZNF274 results in the transcriptional activation of genomic neighbourhoods encompassing, among others, zinc finger and protocadherin-encoding genes, with loss of H3K9me3 repressive mark, altered 3D genome conformation and de novo CTCF binding. In contrast to other factors that have been implicated in chromatin anchoring, ZNF274 is necessary both for transcriptional silencing and nucleolar tethering. While the establishment of silencing depends on the KRAB domain, we demonstrate that the SCAN domain is required to gather ZNF274 complexes at the nucleolus and efficiently spread heterochromatin. Thus, ZNF274 orchestrates the segregation of developmentally regulated gene clusters at nucleoli to allow timely and selective activation of cell-restricted alleles. Overall design: HiC and UMI4C in HEK293T in WT, ZNF274KO conditions
SAMPLE_TITLE: HiC in ZNF274KO 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HEK293T"}, {"TAG": "cell line", "VALUE": "HEK293T"}, {"TAG": "genotype", "VALUE": "ZNF274KO"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: HiC in ZNF274KO 2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC in ZNF274KO 2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "set2_8718_S6_R1.fastq.gz", "size": "15557151233", "date": "2023-06-07 23:31:46", "md5": "e4ba8aab324b32ee8376e3c48a67a4b3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "set2_8718_S6_R2.fastq.gz", "size": "16314877003", "date": "2023-06-07 23:32:54", "md5": "e38ebe336879ed340a389cb88dbea249", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR24871443", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24871443/SRR24871443", "size": "17934265762", "date": "2023-06-07 23:36:08", "md5": "2e9f87ebb11d3ad854229e050152023e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR24871443.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR024/24871/SRR24871443/SRR24871443.lite.1", "size": "14448634230", "date": "2023-06-13 05:12:40", "md5": "70eec4f9cda05cf49ca2e75d61b04b88", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]