{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2075SWXE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2075SWXE",
"aliases": [
"igvf:multiome_scrna_seq"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"ERROR": [
{
"category": "inconsistent preferred assay title",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has `assay_term` single-cell RNA sequencing assay, but `preferred_assay_title` scRNA-seq. Measurement sets are expected to specify an appropriate preferred assay title for its respective assay term.",
"level": 60,
"level_name": "ERROR",
"name": "audit_preferred_assay_title",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "unexpected multiome size",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has `multiome_size`. Only measurement sets from multiome assays are expected to specify a multiome size.",
"level": 60,
"level_name": "ERROR",
"name": "audit_related_multiome_datasets",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "inconsistent multiome datasets",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has a `multiome_size` of 2, but no `related_multiome_datasets`. Measurement sets with a multiome size are expected to have the corresponding amount of measurement sets (excluding itself) listed in related multiome datasets. Each of these datasets are expected to have the same multiome size and samples.",
"level": 60,
"level_name": "ERROR",
"name": "audit_related_multiome_datasets",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "inconsistent related donors",
"detail": "Human donor [IGVFDO2718IDDQ](/human-donors/IGVFDO2718IDDQ/) has [IGVFDO6638HIAD](/human-donors/IGVFDO6638HIAD/) as a related donor, but [IGVFDO6638HIAD](/human-donors/IGVFDO6638HIAD/) does not mutually specify [IGVFDO2718IDDQ](/human-donors/IGVFDO2718IDDQ/) as a related donor in `related_donors`. The human donors indicated in the list of related donors are expected to include a mutual link to the corresponding donor.",
"level": 60,
"level_name": "ERROR",
"name": "audit_related_donors",
"path": "/human-donors/IGVFDO2718IDDQ/"
}
],
"INTERNAL_ACTION": [
{
"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/"
},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO2722UPGC](/human-donors/IGVFDO2722UPGC/) has in progress subobject publication [c81fcd72-95c5-4c19-99f9-270258cf53ef](/publications/c81fcd72-95c5-4c19-99f9-270258cf53ef/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO2722UPGC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has in progress subobject multiplexed sample [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has deleted subobject human donor [IGVFDO9992MNXH](/human-donors/IGVFDO9992MNXH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO2718IDDQ](/human-donors/IGVFDO2718IDDQ/) has in progress subobject document [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO2718IDDQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing barcode map",
"detail": "Multiplexed sample [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/) has no `barcode_map`. Multiplexed samples that use barcodes for demultiplexing are expected to specify a barcode map.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_multiplexed_sample_no_barcode_map",
"path": "/multiplexed-samples/IGVFSM5402QIAO/"
},
{
"category": "missing files",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing NIH certification",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has a sample [IGVFSM8951NUIN](/in-vitro-systems/IGVFSM8951NUIN/) that is multiplexed in [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/) that lacks any `institutional_certificates` issued to the lab that submitted this file set or to a partner lab/award of the submitting lab. Measurement sets for mapping assays or controlled access characterization assays involving samples with a human origin are expected to link to the relevant institutional certificates.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing NIH certification",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has a sample [IGVFSM7924JBAJ](/in-vitro-systems/IGVFSM7924JBAJ/) that is multiplexed in [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/) that lacks any `institutional_certificates` issued to the lab that submitted this file set or to a partner lab/award of the submitting lab. Measurement sets for mapping assays or controlled access characterization assays involving samples with a human origin are expected to link to the relevant institutional certificates.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing NIH certification",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has a sample [IGVFSM9759PRSH](/in-vitro-systems/IGVFSM9759PRSH/) that is multiplexed in [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/) that lacks any `institutional_certificates` issued to the lab that submitted this file set or to a partner lab/award of the submitting lab. Measurement sets for mapping assays or controlled access characterization assays involving samples with a human origin are expected to link to the relevant institutional certificates.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing NIH certification",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has a sample [IGVFSM7317MBCX](/primary-cells/IGVFSM7317MBCX/) that is multiplexed in [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/) that lacks any `institutional_certificates` issued to the lab that submitted this file set or to a partner lab/award of the submitting lab. Measurement sets for mapping assays or controlled access characterization assays involving samples with a human origin are expected to link to the relevant institutional certificates.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing NIH certification",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has a sample [IGVFSM6540QIDH](/tissues/IGVFSM6540QIDH/) that is multiplexed in [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/) that lacks any `institutional_certificates` issued to the lab that submitted this file set or to a partner lab/award of the submitting lab. Measurement sets for mapping assays or controlled access characterization assays involving samples with a human origin are expected to link to the relevant institutional certificates.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing NIH certification",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has a sample [IGVFSM5728BQOF](/in-vitro-systems/IGVFSM5728BQOF/) that is multiplexed in [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/) that lacks any `institutional_certificates` issued to the lab that submitted this file set or to a partner lab/award of the submitting lab. Measurement sets for mapping assays or controlled access characterization assays involving samples with a human origin are expected to link to the relevant institutional certificates.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has an `assay_term` of single-cell RNA sequencing assay but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS2075SWXE/"
},
{
"category": "missing protocol",
"detail": "Measurement set [IGVFDS2075SWXE](/measurement-sets/IGVFDS2075SWXE/) has no `protocols`. Measurement sets are expected to specify the experimental protocol utilized for conducting the assay on protocols.io.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_unspecified_protocol",
"path": "/measurement-sets/IGVFDS2075SWXE/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "Multiplexed sample [IGVFSM5402QIAO](/multiplexed-samples/IGVFSM5402QIAO/) 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": "/multiplexed-samples/IGVFSM5402QIAO/"
}
]
},
"award": {
"@id": "/awards/HG012051/",
"component": "networks",
"contact_pi": {
"@id": "/users/7138e67a-2af5-4a48-90bc-04ea95b53c78/",
"title": "Danwei Huangfu"
},
"title": "Genomic control of gene regulatory networks governing early human lineage decisions"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0948BMCL/",
"accession": "IGVFDS0948BMCL",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/reference-files/IGVFFI4139LADO/",
"accession": "IGVFFI4139LADO",
"content_type": "genome reference",
"status": "in progress",
"summary": "genome reference"
}
],
"status": "in progress",
"summary": "guide (sgRNA) library targeting TF binding sites, phenotype-associated variants genome-wide associated with DiGeorge syndrome"
}
],
"control_for": [],
"creation_timestamp": "2023-04-27T18:51:25.517421+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0965QSBA/",
"accession": "IGVFDO0965QSBA",
"aliases": [
"igvf:donor_of_HUDEP-2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9992MNXH/",
"accession": "IGVFDO9992MNXH",
"aliases": [
"danwei-huangfu:donor_HUES8"
],
"sex": "male",
"status": "deleted",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2722UPGC/",
"accession": "IGVFDO2722UPGC",
"aliases": [
"igvf:donor_of_HAP-1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS7313RRWQ/"
],
"lab": {
"@id": "/labs/danwei-huangfu/",
"title": "Danwei Huangfu, MSKCC"
},
"multiome_size": 2,
"preferred_assay_title": "scRNA-seq",
"related_multiome_datasets": [],
"release_timestamp": "2023-04-27T18:51:25.501042+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM5402QIAO/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM5402QIAO",
"aliases": [
"igvf:multiplexed_sample_example_01"
],
"cellular_sub_pool": "52T_A",
"classifications": [
"cell line",
"differentiated cell specimen",
"primary cell",
"tissue",
"multiplexed sample"
],
"disease_terms": [
{
"@id": "/phenotype-terms/MONDO_0005258/",
"status": "in progress",
"term_name": "autism spectrum disorder"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/991b7ad5-72dc-4724-8cf1-b62f0cfa08b8/",
"certificate_identifier": "IP123-99",
"controlled_access": true,
"data_use_limitation": "DS",
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000115/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "in progress",
"summary": "endothelial cell",
"term_name": "endothelial cell"
},
{
"@id": "/sample-terms/CL_0000540/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "in progress",
"summary": "neuron",
"term_name": "neuron"
},
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
},
{
"@id": "/sample-terms/EFO_0007598/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HAP-1"
],
"status": "released",
"summary": "HAP-1",
"term_name": "HAP-1"
},
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "in progress",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
},
{
"@id": "/sample-terms/UBERON_0001898/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "in progress",
"summary": "hypothalamus",
"term_name": "hypothalamus"
}
],
"status": "in progress",
"summary": "multiplexed sample: Homo sapiens (female) H9 differentiated cell specimen induced to neural progenitor cell for 30 minutes (cellular sub pool: K80_A2); Homo sapiens (male) endothelial cell line (sorting details: detail of the fraction) depleted of lipopolysaccharide for 6 hours, transfected with a guide library; ... and 4 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/fbf87db1-7a2f-46de-9723-f76dea8669b2/",
"purpose": "activation",
"status": "in progress",
"summary": "Depletion of lipopolysaccharide for 6 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/1e75d989-a438-4d77-a451-8a297fd3636e/",
"title": "Ian Whaling"
},
"summary": "CRISPR scRNA-seq integrating a guide (sgRNA) library targeting TF binding sites, phenotype-associated variants genome-wide associated with DiGeorge syndrome",
"uuid": "4102848f-4d47-4fd4-9491-b77ce7c9dbb1"
}