{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1338GOGT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1338GOGT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"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 [IGVFDS1338GOGT](/measurement-sets/IGVFDS1338GOGT/) links to sample [IGVFSM5613UEVU](/in-vitro-systems/IGVFSM5613UEVU/) which links to auxiliary set [IGVFDS1546MEZJ](/auxiliary-sets/IGVFDS1546MEZJ/) 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/IGVFDS1338GOGT/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1338GOGT](/measurement-sets/IGVFDS1338GOGT/) 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/IGVFDS1338GOGT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1338GOGT](/measurement-sets/IGVFDS1338GOGT/) has sequence file(s) [IGVFFI0621LSOC](/sequence-files/IGVFFI0621LSOC/), [IGVFFI6147WPCX](/sequence-files/IGVFFI6147WPCX/), [IGVFFI5037ZQHU](/sequence-files/IGVFFI5037ZQHU/), [IGVFFI6991LZWF](/sequence-files/IGVFFI6991LZWF/) 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/IGVFDS1338GOGT/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1338GOGT](/measurement-sets/IGVFDS1338GOGT/) has revoked subobject auxiliary set [IGVFDS0241XMRI](/auxiliary-sets/IGVFDS0241XMRI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1338GOGT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5613UEVU](/in-vitro-systems/IGVFSM5613UEVU/) 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/IGVFSM5613UEVU/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS0241XMRI](/auxiliary-sets/IGVFDS0241XMRI/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS0241XMRI/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1338GOGT](/measurement-sets/IGVFDS1338GOGT/) 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/IGVFDS1338GOGT/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5613UEVU](/in-vitro-systems/IGVFSM5613UEVU/) 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/IGVFSM5613UEVU/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0241XMRI/",
"accession": "IGVFDS0241XMRI",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"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": "2024-05-14T20:32:53.885931+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI7183LNMQ/",
"accession": "IGVFFI7183LNMQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:54.406379+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI7183LNMQ/@@download/IGVFFI7183LNMQ.yaml.gz",
"md5sum": "2412838da77d2ce715bc86afc8ff126a",
"s3_uri": "s3://igvf-files/2024/06/11/f8f0db89-55a3-40a9-8a7a-0d9d867fc120/IGVFFI7183LNMQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4956UORA/",
"accession": "IGVFFI4956UORA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:38.740871+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI4956UORA/@@download/IGVFFI4956UORA.yaml.gz",
"md5sum": "24b95cfd255332f3eccc81832b4c6f92",
"s3_uri": "s3://igvf-files/2024/06/11/3e229ff2-e583-49ea-bbc2-60570c5139d4/IGVFFI4956UORA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0621LSOC/",
"accession": "IGVFFI0621LSOC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:20.782784+00:00",
"file_format": "fastq",
"file_size": 10270135,
"href": "/sequence-files/IGVFFI0621LSOC/@@download/IGVFFI0621LSOC.fastq.gz",
"md5sum": "b11048301a203828caabad8e93c79647",
"s3_uri": "s3://igvf-files/2024/06/01/90e3c3f6-a23b-444e-adcb-5414c7b9863f/IGVFFI0621LSOC.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-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0566CKPJ/",
"accession": "IGVFFI0566CKPJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:37:24.308232+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0566CKPJ/@@download/IGVFFI0566CKPJ.yaml.gz",
"md5sum": "62acf469b930e4a9e7da2c0bf7f4757a",
"s3_uri": "s3://igvf-files/2024/06/11/b2867c65-688d-4952-b116-8cff93986f84/IGVFFI0566CKPJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5999FTUB/",
"accession": "IGVFFI5999FTUB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:09.823794+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5999FTUB/@@download/IGVFFI5999FTUB.yaml.gz",
"md5sum": "ced7a7d469b8fbac0caf3385a10e27ef",
"s3_uri": "s3://igvf-files/2024/06/11/2a75c8b3-d34a-4994-b09f-172235671887/IGVFFI5999FTUB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI6147WPCX/",
"accession": "IGVFFI6147WPCX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:38.833879+00:00",
"file_format": "fastq",
"file_size": 14757260,
"href": "/sequence-files/IGVFFI6147WPCX/@@download/IGVFFI6147WPCX.fastq.gz",
"md5sum": "89278642f93ad4ebe7ad428368f6e950",
"s3_uri": "s3://igvf-files/2024/06/01/e0d37963-0115-4ed3-8ebb-aacd973cb2b0/IGVFFI6147WPCX.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-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5037ZQHU/",
"accession": "IGVFFI5037ZQHU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:44:44.451017+00:00",
"file_format": "fastq",
"file_size": 6850184,
"href": "/sequence-files/IGVFFI5037ZQHU/@@download/IGVFFI5037ZQHU.fastq.gz",
"md5sum": "e0ae00d691c06c3ba09e16e5b25d2c89",
"s3_uri": "s3://igvf-files/2024/06/01/6f1e0f19-03b8-42e9-932e-90beca84db64/IGVFFI5037ZQHU.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-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6991LZWF/",
"accession": "IGVFFI6991LZWF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:45:03.419803+00:00",
"file_format": "fastq",
"file_size": 7043597,
"href": "/sequence-files/IGVFFI6991LZWF/@@download/IGVFFI6991LZWF.fastq.gz",
"md5sum": "f8d7020812e119e9a90e7733155a2446",
"s3_uri": "s3://igvf-files/2024/06/01/d32a906a-e85c-4daf-a321-a110fae60587/IGVFFI6991LZWF.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-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10_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": "2024-07-10T19:51:05.077022+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5613UEVU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5613UEVU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR1-Rep1_S4",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR2-Rep1_S10",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR3-Rep1_S58",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinD-PCR4-Rep1_S64"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"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) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, 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": "2024-06-01T01:44:44.451017+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": "2d9aab23-3773-4442-9847-26ee8382e115"
}