{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8252XAWN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8252XAWN",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin3"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8252XAWN](/measurement-sets/IGVFDS8252XAWN/) has in progress subobject publication [2e37380f-fb50-4dbc-a7ec-e9e6532c9f99](/publications/2e37380f-fb50-4dbc-a7ec-e9e6532c9f99/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8252XAWN/"
},
{
"category": "mismatched status",
"detail": "Released auxiliary set [IGVFDS9830AWTI](/auxiliary-sets/IGVFDS9830AWTI/) has in progress subobject publication [2e37380f-fb50-4dbc-a7ec-e9e6532c9f99](/publications/2e37380f-fb50-4dbc-a7ec-e9e6532c9f99/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/auxiliary-sets/IGVFDS9830AWTI/"
},
{
"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 auxiliary set",
"detail": "Measurement set [IGVFDS8252XAWN](/measurement-sets/IGVFDS8252XAWN/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS8252XAWN/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS8252XAWN](/measurement-sets/IGVFDS8252XAWN/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS8252XAWN/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9830AWTI](/auxiliary-sets/IGVFDS9830AWTI/) has sequence file(s) [IGVFFI1386DIXA](/sequence-files/IGVFFI1386DIXA/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS9830AWTI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9830AWTI](/auxiliary-sets/IGVFDS9830AWTI/) has sequence file(s): [IGVFFI1386DIXA](/sequence-files/IGVFFI1386DIXA/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS9830AWTI/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9830AWTI/",
"accession": "IGVFDS9830AWTI",
"aliases": [
"jesse-engreitz:auxiliary_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin3"
],
"file_set_type": "gRNA sequencing"
}
],
"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"
},
"control_for": [],
"creation_timestamp": "2024-01-12T20:51:02.070101+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS9053MHCS/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"publications": [
{
"@id": "/publications/2e37380f-fb50-4dbc-a7ec-e9e6532c9f99/",
"publication_identifiers": [
"PMID:38326615"
]
}
],
"release_timestamp": "2024-02-07T19:07:03.637882+00:00",
"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"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7621RRLM/",
"accession": "IGVFDS7621RRLM",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference"
}
],
"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"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/4b2083b4-24c1-41d8-9daa-e79299f00d6e/",
"title": "Ronghao Zhou"
},
"submitted_files_timestamp": "2023-12-05T00:44:41.167436+00:00",
"summary": "CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus",
"uuid": "59bf770f-5e53-4612-b1f8-ab1bd6f3a2ad"
}