EXPERIMENT_TITLE: iPSC Hi-C: Sample c05e2bef-3b5b-43cf-b93e-cc6508fd1a93
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The iPSCORE Resource of human induced pluripotent stem cells (hiPSCs) was created as part of the Next-Gen Consortium funded by the NHLBI. The overarching purpose of the iPSCORE Resource is to provide a large collection of hiPSCs for use in studying the impact of genetic variation on molecular and physiological phenotypes. This Resource is being used in a number of ongoing studies for which genomic data will be generated and deposited into public repositories and linked through dbGaP. A total of 273 individuals have participated in the study for which 222 have had hiPSCs generated from fibroblasts (available through WiCell (http://www.wicell.org/)). Of the 273 individuals, 181 are part of 55 families that include 24 monozygotic twin pairs and 5 dizygotic twin pairs, allowing for the incorporation of familial relationships into genetic analyses. Germline DNA has been sequenced from blood or fibroblast samples for all 273 individuals (see http://www.ncbi... (for more see dbGaP study page.)
SAMPLE_TITLE: Non-tumor DNA sample from a human male participant in the dbGaP study "NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource for Studying the Impact of Genetic Variation on Molecular Phenotypes"
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "gap_accession", "VALUE": "phs000924"}, {"TAG": "submitter handle", "VALUE": "iPSCORE"}, {"TAG": "biospecimen repository", "VALUE": "iPSCORE"}, {"TAG": "study name", "VALUE": "NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource for Studying the Impact of Genetic Variation on Molecular Phenotypes"}, {"TAG": "study design", "VALUE": "Control Set"}, {"TAG": "biospecimen repository sample id", "VALUE": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93"}, {"TAG": "submitted sample id", "VALUE": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93"}, {"TAG": "submitted subject id", "VALUE": "f549b5fa-a6c0-49fb-8a07-dda4f72ff076"}, {"TAG": "gap_sample_id", "VALUE": "3300009"}, {"TAG": "gap_subject_id", "VALUE": "2048594"}, {"TAG": "sex", "VALUE": "male"}, {"TAG": "histological type", "VALUE": "iPSC"}, {"TAG": "analyte type", "VALUE": "DNA"}, {"TAG": "is tumor", "VALUE": "No"}, {"TAG": "gap_consent_code", "VALUE": "1"}, {"TAG": "gap_consent_short_name", "VALUE": "GRU"}]
Pool_Member_@attributes_sample_title: Non-tumor DNA sample from a human male participant in the dbGaP study "NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource for Studying the Impact of Genetic Variation on Molecular Phenotypes"
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR8419619", "SUBMITTER_ID": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93_files"}, "EXPERIMENT_REF": {"IDENTIFIERS": {"SUBMITTER_ID": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93"}, "@attributes": {"accession": "SRX5228669"}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS4232444", "EXTERNAL_ID": ["SAMN10137419", "924-c05e2bef-3b5b-43cf-b93e-cc6508fd1a93", "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93"]}, "@attributes": {"member_name": "", "accession": "SRS4232444", "sample_name": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93", "sample_title": "Non-tumor DNA sample from a human male participant in the dbGaP study \"NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource for Studying the Impact of Genetic Variation on Molecular Phenotypes\"", "spots": "233845655", "bases": "34984356189", "tax_id": "9606", "organism": "Homo sapiens"}}}, "AlignInfo": {"Alignment": [null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null], "@attributes": {"cnt": "93"}}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": null, "@attributes": {"nreads": "1", "nspots": "233845655"}}, "Databases": {"Database": {"Table": [{"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "PRIMARY_ALIGNMENT"}}, {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "REFERENCE"}}, {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "SECONDARY_ALIGNMENT"}}, {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "SEQUENCE"}}]}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "34984356189"}}, "@attributes": {"accession": "SRR8419619", "alias": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93_files", "total_spots": "233845655", "total_bases": "34984356189", "size": "10242438095", "load_done": "true", "published": "2019-03-06 18:50:12", "is_public": "true", "cluster_name": "dbgap", "has_taxanalysis": "1", "assembly": "hg19"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR8539633", "SUBMITTER_ID": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93_files_reverse"}, "EXPERIMENT_REF": {"IDENTIFIERS": {"SUBMITTER_ID": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93"}, "@attributes": {"accession": "SRX5228669"}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS4232444", "EXTERNAL_ID": ["SAMN10137419", "924-c05e2bef-3b5b-43cf-b93e-cc6508fd1a93", "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93"]}, "@attributes": {"member_name": "", "accession": "SRS4232444", "sample_name": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93", "sample_title": "Non-tumor DNA sample from a human male participant in the dbGaP study \"NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource for Studying the Impact of Genetic Variation on Molecular Phenotypes\"", "spots": "233845655", "bases": "34982875854", "tax_id": "9606", "organism": "Homo sapiens"}}}, "AlignInfo": {"Alignment": [null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null], "@attributes": {"cnt": "93"}}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": null, "@attributes": {"nreads": "1", "nspots": "233845655"}}, "Databases": {"Database": {"Table": [{"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "PRIMARY_ALIGNMENT"}}, {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "REFERENCE"}}, {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "SECONDARY_ALIGNMENT"}}, {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "SEQUENCE"}}]}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "34982875854"}}, "@attributes": {"alias": "c05e2bef-3b5b-43cf-b93e-cc6508fd1a93_files_reverse", "accession": "SRR8539633", "total_spots": "233845655", "total_bases": "34982875854", "size": "12786187426", "load_done": "true", "published": "2019-03-06 18:50:12", "is_public": "true", "cluster_name": "dbgap", "has_taxanalysis": "1", "assembly": "hg19"}}]