{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS9053MHCS/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9053MHCS",
"aliases": [
"jesse-engreitz:analysis_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_analysis"
],
"assay_titles": [
"CRISPR FlowFISH screen"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS9053MHCS](/analysis-sets/IGVFDS9053MHCS/) links to file set(s): [IGVFDS4378DCUS](/measurement-sets/IGVFDS4378DCUS/), [IGVFDS0071OLHI](/measurement-sets/IGVFDS0071OLHI/), [IGVFDS9231LVGR](/measurement-sets/IGVFDS9231LVGR/), [IGVFDS0018LXFE](/measurement-sets/IGVFDS0018LXFE/), [IGVFDS8508PSMW](/measurement-sets/IGVFDS8508PSMW/), [IGVFDS6709HOZL](/measurement-sets/IGVFDS6709HOZL/), [IGVFDS2108LFDU](/measurement-sets/IGVFDS2108LFDU/), [IGVFDS8529BNPK](/measurement-sets/IGVFDS8529BNPK/), [IGVFDS0882RKGQ](/measurement-sets/IGVFDS0882RKGQ/), [IGVFDS6694UWZS](/measurement-sets/IGVFDS6694UWZS/), [IGVFDS2367NFMX](/measurement-sets/IGVFDS2367NFMX/), [IGVFDS8252XAWN](/measurement-sets/IGVFDS8252XAWN/), [IGVFDS1890YDYU](/measurement-sets/IGVFDS1890YDYU/), [IGVFDS2419JZMR](/measurement-sets/IGVFDS2419JZMR/), [IGVFDS3115BOGO](/measurement-sets/IGVFDS3115BOGO/), [IGVFDS8329NAOV](/measurement-sets/IGVFDS8329NAOV/) in `input_file_sets` that are not represented in the `derived_from` of the file sets of the files in this analysis. The analysis set input files are expected to belong to the input file sets.",
"level": 60,
"level_name": "ERROR",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/IGVFDS9053MHCS/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released analysis set [IGVFDS9053MHCS](/analysis-sets/IGVFDS9053MHCS/) has in progress subobject publication [ab9749d9-4092-4a1a-b74f-b50f1164e659](/publications/ab9749d9-4092-4a1a-b74f-b50f1164e659/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/analysis-sets/IGVFDS9053MHCS/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000753/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Analysis set [IGVFDS9053MHCS](/analysis-sets/IGVFDS9053MHCS/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/analysis-sets/IGVFDS9053MHCS/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5229SOKC](/in-vitro-systems/IGVFSM5229SOKC/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM5229SOKC/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3508ZAFL](/in-vitro-systems/IGVFSM3508ZAFL/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM3508ZAFL/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8121JQAK](/in-vitro-systems/IGVFSM8121JQAK/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM8121JQAK/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9054OJLH](/in-vitro-systems/IGVFSM9054OJLH/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM9054OJLH/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2155YTIW](/in-vitro-systems/IGVFSM2155YTIW/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM2155YTIW/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5826EWDE](/in-vitro-systems/IGVFSM5826EWDE/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM5826EWDE/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2756NFXE](/in-vitro-systems/IGVFSM2756NFXE/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM2756NFXE/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6408QEFG](/in-vitro-systems/IGVFSM6408QEFG/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM6408QEFG/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8115WXZU](/in-vitro-systems/IGVFSM8115WXZU/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM8115WXZU/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6467VTYE](/in-vitro-systems/IGVFSM6467VTYE/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM6467VTYE/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6823DARA](/in-vitro-systems/IGVFSM6823DARA/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM6823DARA/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5424HTHI](/in-vitro-systems/IGVFSM5424HTHI/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM5424HTHI/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7319EZLZ](/in-vitro-systems/IGVFSM7319EZLZ/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM7319EZLZ/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9750UXVD](/in-vitro-systems/IGVFSM9750UXVD/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM9750UXVD/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM0599MHTG](/in-vitro-systems/IGVFSM0599MHTG/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM0599MHTG/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7436UMQD](/in-vitro-systems/IGVFSM7436UMQD/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM7436UMQD/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7621RRLM/",
"accession": "IGVFDS7621RRLM",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI1837MRQJ/",
"accession": "IGVFFI1837MRQJ",
"content_type": "guide RNA sequences",
"status": "deleted",
"summary": "GRCh38 guide RNA sequences"
},
{
"@id": "/tabular-files/IGVFFI9333CGMN/",
"accession": "IGVFFI9333CGMN",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus"
}
],
"control_for": [],
"creation_timestamp": "2024-01-16T22:38:02.756733+00:00",
"description": "Analysis of TLNRD1 CRIPSRi enhancer screen with FlowFISH in TeloHAEC",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS8529BNPK/",
"accession": "IGVFDS8529BNPK",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep1_bin1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8329NAOV/",
"accession": "IGVFDS8329NAOV",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep1_bin2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0071OLHI/",
"accession": "IGVFDS0071OLHI",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep1_bin3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6709HOZL/",
"accession": "IGVFDS6709HOZL",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep1_bin4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2367NFMX/",
"accession": "IGVFDS2367NFMX",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0882RKGQ/",
"accession": "IGVFDS0882RKGQ",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8252XAWN/",
"accession": "IGVFDS8252XAWN",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6694UWZS/",
"accession": "IGVFDS6694UWZS",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8508PSMW/",
"accession": "IGVFDS8508PSMW",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep3_bin1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3115BOGO/",
"accession": "IGVFDS3115BOGO",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep3_bin2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4378DCUS/",
"accession": "IGVFDS4378DCUS",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep3_bin3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9231LVGR/",
"accession": "IGVFDS9231LVGR",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep3_bin4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1890YDYU/",
"accession": "IGVFDS1890YDYU",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2108LFDU/",
"accession": "IGVFDS2108LFDU",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0018LXFE/",
"accession": "IGVFDS0018LXFE",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2419JZMR/",
"accession": "IGVFDS2419JZMR",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin4"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "This object's file_set_type was primary analysis and has been updated to be principal analysis.",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"publications": [
{
"@id": "/publications/ab9749d9-4092-4a1a-b74f-b50f1164e659/",
"publication_identifiers": [
"PMID:37733863",
"doi:10.1126/science.adg7492"
],
"status": "in progress"
}
],
"release_timestamp": "2024-02-07T18:50:00.110075+00:00",
"sample_summary": "TeloHAEC cell line, modified with CRISPR modifications, transfected with a guide library, sorted on expression of TLNRD1",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9054OJLH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9054OJLH",
"aliases": [
"jesse-engreitz:in-vitro-system_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin3"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin for 51-75% expression of TLNRD1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2756NFXE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2756NFXE",
"aliases": [
"jesse-engreitz:in-vitro-system_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep1_bin3"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin for 51-75% expression of TLNRD1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM6823DARA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6823DARA",
"aliases": [
"jesse-engreitz:in-vitro-system_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep1_bin4"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin for 76-100% expression of TLNRD1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM2155YTIW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2155YTIW",
"aliases": [
"jesse-engreitz:in-vitro-system_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin1"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin for 0-25% expression of TLNRD1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM5424HTHI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5424HTHI",
"aliases": [
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"title": "Ronghao Zhou"
},
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}