{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1334EHAI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1334EHAI",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"ERROR": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1334EHAI](/measurement-sets/IGVFDS1334EHAI/) links to sample [IGVFSM6629TXKH](/in-vitro-systems/IGVFSM6629TXKH/) which links to auxiliary set [IGVFDS6020CDHF](/auxiliary-sets/IGVFDS6020CDHF/) but is not in its `auxiliary_sets`. Measurement sets are expected to link to auxiliary sets if they share the same sample.",
"level": 60,
"level_name": "ERROR",
"name": "audit_missing_auxiliary_set_link",
"path": "/measurement-sets/IGVFDS1334EHAI/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6629TXKH](/in-vitro-systems/IGVFSM6629TXKH/) 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/IGVFSM6629TXKH/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1334EHAI](/measurement-sets/IGVFDS1334EHAI/) 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/IGVFDS1334EHAI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1334EHAI](/measurement-sets/IGVFDS1334EHAI/) has sequence file(s) [IGVFFI0315AYNG](/sequence-files/IGVFFI0315AYNG/), [IGVFFI4529YFBY](/sequence-files/IGVFFI4529YFBY/), [IGVFFI5357ACRU](/sequence-files/IGVFFI5357ACRU/), [IGVFFI9488COAD](/sequence-files/IGVFFI9488COAD/) 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/IGVFDS1334EHAI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1334EHAI](/measurement-sets/IGVFDS1334EHAI/) has revoked subobject auxiliary set [IGVFDS0791JOAT](/auxiliary-sets/IGVFDS0791JOAT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1334EHAI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS0791JOAT](/auxiliary-sets/IGVFDS0791JOAT/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS0791JOAT/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6629TXKH](/in-vitro-systems/IGVFSM6629TXKH/) 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/IGVFSM6629TXKH/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1334EHAI](/measurement-sets/IGVFDS1334EHAI/) 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/IGVFDS1334EHAI/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0791JOAT/",
"accession": "IGVFDS0791JOAT",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"file_set_type": "gRNA sequencing",
"status": "revoked"
}
],
"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": "2024-05-14T20:54:41.971100+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/IGVFFI5152ILXJ/",
"accession": "IGVFFI5152ILXJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:06.452882+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5152ILXJ/@@download/IGVFFI5152ILXJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/27404c44-2f76-48a8-b0cc-490da7f5cb4a/IGVFFI5152ILXJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4931FRCX/",
"accession": "IGVFFI4931FRCX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:50.866992+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4931FRCX/@@download/IGVFFI4931FRCX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/15edf48c-e15a-4d12-bfb7-ce8d603a2982/IGVFFI4931FRCX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0315AYNG/",
"accession": "IGVFFI0315AYNG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:32.363139+00:00",
"file_format": "fastq",
"file_size": 16567622,
"href": "/sequence-files/IGVFFI0315AYNG/@@download/IGVFFI0315AYNG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/df90e240-b153-42df-bd65-c19233f778c2/IGVFFI0315AYNG.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-FF1-BinD-PCR2-Rep1_S34_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9103TGSJ/",
"accession": "IGVFFI9103TGSJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:21.484640+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI9103TGSJ/@@download/IGVFFI9103TGSJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8c041cfc-6f96-423e-b150-3456c45d577d/IGVFFI9103TGSJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6811NNBT/",
"accession": "IGVFFI6811NNBT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:37.409077+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6811NNBT/@@download/IGVFFI6811NNBT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e148f6bf-93ae-4290-aecc-858fa7b83a30/IGVFFI6811NNBT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4529YFBY/",
"accession": "IGVFFI4529YFBY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:14.110692+00:00",
"file_format": "fastq",
"file_size": 17739882,
"href": "/sequence-files/IGVFFI4529YFBY/@@download/IGVFFI4529YFBY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c9530500-38be-45c4-bf47-98ed65d23a24/IGVFFI4529YFBY.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-FF1-BinD-PCR1-Rep1_S28_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5357ACRU/",
"accession": "IGVFFI5357ACRU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:50.570946+00:00",
"file_format": "fastq",
"file_size": 26008308,
"href": "/sequence-files/IGVFFI5357ACRU/@@download/IGVFFI5357ACRU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a88f1e2b-fa50-49f4-98ff-8ad9fb51866b/IGVFFI5357ACRU.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-FF1-BinD-PCR3-Rep1_S82_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9488COAD/",
"accession": "IGVFFI9488COAD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:09.079191+00:00",
"file_format": "fastq",
"file_size": 21674394,
"href": "/sequence-files/IGVFFI9488COAD/@@download/IGVFFI9488COAD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d658e637-4f85-4b0e-9c49-9f3ff149fea8/IGVFFI9488COAD.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-FF1-BinD-PCR4-Rep1_S88_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": "2024-07-10T19:52:24.737587+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6629TXKH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6629TXKH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR1-Rep1_S28",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR2-Rep1_S34",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR3-Rep1_S82",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinD-PCR4-Rep1_S88"
],
"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": "2024-06-01T01:47:14.110692+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": "4342072d-8684-4be0-852e-bfbd7b4f69a9"
}