{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3115IMKA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3115IMKA",
"aliases": [
"jesse-engreitz:measurement_NOS3_CRISPRi_FF_R1_FFrep2_binB_PCR1_S122"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4464SPLF](/in-vitro-systems/IGVFSM4464SPLF/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM4464SPLF/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3115IMKA](/measurement-sets/IGVFDS3115IMKA/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS3115IMKA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3115IMKA](/measurement-sets/IGVFDS3115IMKA/) has sequence file(s): [IGVFFI8892HDLR](/sequence-files/IGVFFI8892HDLR/), [IGVFFI9930DDID](/sequence-files/IGVFFI9930DDID/), [IGVFFI9172KREC](/sequence-files/IGVFFI9172KREC/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3115IMKA/"
},
{
"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/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM4464SPLF](/in-vitro-systems/IGVFSM4464SPLF/) 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/IGVFSM4464SPLF/"
},
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS3115IMKA](/measurement-sets/IGVFDS3115IMKA/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS3115IMKA/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3115IMKA](/measurement-sets/IGVFDS3115IMKA/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS3115IMKA/"
}
]
},
"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/IGVFDS8953DFJK/",
"accession": "IGVFDS8953DFJK",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5833LNWN/",
"accession": "IGVFFI5833LNWN",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3"
}
],
"control_for": [],
"creation_timestamp": "2024-04-16T14:54:09.751040+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"documents": [
"/documents/1d492aa4-f111-4220-aeaa-f43a3cbda78b/"
],
"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": [
{
"@id": "/sequence-files/IGVFFI8892HDLR/",
"accession": "IGVFFI8892HDLR",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:27.490523+00:00",
"file_format": "fastq",
"file_size": 29042050,
"href": "/sequence-files/IGVFFI8892HDLR/@@download/IGVFFI8892HDLR.fastq.gz",
"md5sum": "6bef8159c9954fae768ae6621774ec2a",
"s3_uri": "s3://igvf-files/2024/04/16/9a44b3ff-3ead-48b9-9e52-4454a7f19906/IGVFFI8892HDLR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0004205/",
"status": "released",
"term_name": "Illumina MiSeq"
},
"status": "released",
"submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep2-BinB-PCRrep1_S122_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9930DDID/",
"accession": "IGVFFI9930DDID",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:24.680200+00:00",
"file_format": "fastq",
"file_size": 10267019,
"href": "/sequence-files/IGVFFI9930DDID/@@download/IGVFFI9930DDID.fastq.gz",
"md5sum": "684f1fc69efce083a47fb3c9f409c0d5",
"s3_uri": "s3://igvf-files/2024/04/16/adfa9875-f73f-49fb-8a74-6abb782b4e74/IGVFFI9930DDID.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0004205/",
"status": "released",
"term_name": "Illumina MiSeq"
},
"status": "released",
"submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep2-BinB-PCRrep1_S122_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9172KREC/",
"accession": "IGVFFI9172KREC",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:26.072989+00:00",
"file_format": "fastq",
"file_size": 10372555,
"href": "/sequence-files/IGVFFI9172KREC/@@download/IGVFFI9172KREC.fastq.gz",
"md5sum": "5596d3755a20cb0e3e16c75f8cda9bfe",
"s3_uri": "s3://igvf-files/2024/04/16/259d212a-ea0b-4952-9173-d876423f16af/IGVFFI9172KREC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0004205/",
"status": "released",
"term_name": "Illumina MiSeq"
},
"status": "released",
"submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep2-BinB-PCRrep1_S122_I2_001.fastq.g",
"upload_status": "validated"
}
],
"input_for": [],
"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"
],
"release_timestamp": "2024-06-22T00:20:39.725544+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4464SPLF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4464SPLF",
"aliases": [
"jesse-engreitz:in-vitro-system_NOS3_CRISPRi_FF_R1_FFrep2_binB_PCR1_S122"
],
"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": "Homo sapiens (female) TeloHAEC cell line (sorting details: FACS bin B for 26-50% expression of NOS3) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-04-16T21:43:24.680200+00:00",
"summary": "CRISPR interference FlowFISH screen sorted on the expression of NOS3 integrating a guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3",
"targeted_genes": [
{
"@id": "/genes/ENSG00000164867/",
"geneid": "ENSG00000164867",
"name": "nitric oxide synthase 3",
"status": "released",
"symbol": "NOS3",
"synonyms": [
"NOSIII",
"NOS type III",
"ECNOS",
"eNOS",
"EC-NOS",
"nitric oxide synthase 3",
"endothelial NOS",
"nitric oxide synthase 3 (endothelial cell)",
"cNOS",
"constitutive NOS",
"NOS3"
]
}
],
"uuid": "09cb8ece-0d4b-4844-93ea-46cd3c5f294b"
}