EXPERIMENT_TITLE: GSM8030922: K562; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Extraction protocol was performed as described in Gridina. et. al 2021 (PMID: 33743768). Exo-C protocol includes a 3C part followed by exome enrichment. The 3C part was performed either following DNase I protocol as described in Gridina. et. al 2021 (PMID: 33743768), or S1 as described in Gridina. et. al 2023 (PMID: 38072950).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type — whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Through several case studies, we demonstrate how Exo-C's multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders. Overall design: Exo-C protocol includes a 3C part followed by exome enrichment. Applied on a cohort of 66 human samples, including one K562 cell line sample. *************************************************************** Submitter states that missing raw files are due to patient privacy concerns. ***************************************************************
SAMPLE_TITLE: K562
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "K562"}, {"TAG": "cell line", "VALUE": "K562"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: K562
RUN_SET_RUN_Pool_Member_@attributes_sample_title: K562
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR27693255.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR027/27693/SRR27693255/SRR27693255.lite.1", "size": "3778270863", "date": "2024-01-23 08:24:39", "md5": "2fb8f5520c62d4d8e03451f96b347bf3", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR27693255", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR27693255/SRR27693255", "size": "5662052379", "date": "2024-01-23 08:08:20", "md5": "b58fcf1f3ce0c4fa30cde9eeb89e64bc", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "s130_K562-102_2.fq.gz", "size": "4294507564", "date": "2024-01-23 08:07:18", "md5": "48c2c9c93804713c75bc3b0a3383c748", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "s130_K562-102_1.fq.gz", "size": "3772609071", "date": "2024-01-23 08:07:08", "md5": "fa945e7dd0827a94e42112cf6ec35138", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]