{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2363BVTQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2363BVTQ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"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": "Auxiliary set [IGVFDS3809LQRK](/auxiliary-sets/IGVFDS3809LQRK/) 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": "/auxiliary-sets/IGVFDS3809LQRK/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6811XGTM](/in-vitro-systems/IGVFSM6811XGTM/) 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/IGVFSM6811XGTM/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2363BVTQ](/measurement-sets/IGVFDS2363BVTQ/) 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/IGVFDS2363BVTQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2363BVTQ](/measurement-sets/IGVFDS2363BVTQ/) has sequence file(s) [IGVFFI6234KUHQ](/sequence-files/IGVFFI6234KUHQ/), [IGVFFI0065HIAT](/sequence-files/IGVFFI0065HIAT/), [IGVFFI6303UTLS](/sequence-files/IGVFFI6303UTLS/), [IGVFFI8668YDHW](/sequence-files/IGVFFI8668YDHW/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS2363BVTQ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6811XGTM](/in-vitro-systems/IGVFSM6811XGTM/) 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/IGVFSM6811XGTM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3809LQRK/",
"accession": "IGVFDS3809LQRK",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_SSFA2-Auxin6hrs-FF2"
],
"file_set_type": "cell sorting",
"status": "released"
}
],
"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/IGVFDS5413RKIA/",
"accession": "IGVFDS5413RKIA",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5130EWUZ/",
"accession": "IGVFFI5130EWUZ",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-14T20:55:11.086640+00:00",
"documents": [
"/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI1542IONW/",
"accession": "IGVFFI1542IONW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:24.783028+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1542IONW/@@download/IGVFFI1542IONW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/41d3f9da-9be3-440b-ab48-099f9607bab4/IGVFFI1542IONW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2542AYLY/",
"accession": "IGVFFI2542AYLY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:52.877820+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2542AYLY/@@download/IGVFFI2542AYLY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c3fb14bb-0593-4f98-9c91-d26bb9299de4/IGVFFI2542AYLY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3258XDEX/",
"accession": "IGVFFI3258XDEX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:09.232044+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI3258XDEX/@@download/IGVFFI3258XDEX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5b5a354a-e437-4dc5-848f-4ce7483e3756/IGVFFI3258XDEX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI6234KUHQ/",
"accession": "IGVFFI6234KUHQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:49:21.411416+00:00",
"file_format": "fastq",
"file_size": 1568355,
"href": "/sequence-files/IGVFFI6234KUHQ/@@download/IGVFFI6234KUHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/265de1c7-576b-4025-bf6f-0fb1bfe164e8/IGVFFI6234KUHQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6800DDJL/",
"accession": "IGVFFI6800DDJL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:40.208575+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI6800DDJL/@@download/IGVFFI6800DDJL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9b7ef02b-a228-4eb5-a7b9-c9a9534748c4/IGVFFI6800DDJL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0065HIAT/",
"accession": "IGVFFI0065HIAT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:49:02.203495+00:00",
"file_format": "fastq",
"file_size": 19082795,
"href": "/sequence-files/IGVFFI0065HIAT/@@download/IGVFFI0065HIAT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/14b7d4a5-f1f4-42ec-8fcc-f3cd32807ddc/IGVFFI0065HIAT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6303UTLS/",
"accession": "IGVFFI6303UTLS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:27.294717+00:00",
"file_format": "fastq",
"file_size": 10545827,
"href": "/sequence-files/IGVFFI6303UTLS/@@download/IGVFFI6303UTLS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e94ef069-e49a-4b11-8820-0d48030bbe5d/IGVFFI6303UTLS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8668YDHW/",
"accession": "IGVFFI8668YDHW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:45.131380+00:00",
"file_format": "fastq",
"file_size": 1352904,
"href": "/sequence-files/IGVFFI8668YDHW/@@download/IGVFFI8668YDHW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9e34a7cb-f2f2-4dfa-b7bc-782bffab9851/IGVFFI8668YDHW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"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/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:53:01.230008+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6811XGTM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6811XGTM",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR1-Rep1_S40",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR2-Rep1_S46",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR3-Rep1_S94",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinD-PCR4-Rep1_S100"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin D for 55-65% expression of SSFA2) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:48:27.294717+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of ITPRID2 integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000138434/",
"geneid": "ENSG00000138434",
"name": "ITPR interacting domain containing 2",
"status": "released",
"symbol": "ITPRID2",
"synonyms": [
"sperm associated antigen 13",
"ITPR interacting domain containing 2",
"ITPR-interacting domain-containing protein 2",
"SSFA2",
"KRAS-induced actin-interacting protein",
"cleavage signal-1 protein",
"ki-ras-induced actin-interacting protein",
"sperm specific antigen 2",
"ITPRID2",
"SPAG13",
"protein ITPRID2",
"CS-1",
"CS1",
"KRAP"
]
}
],
"uuid": "2b499365-0869-4937-90dd-8172a9e6ae88"
}