{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1261RWQY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1261RWQY",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR1-Rep1_S29",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR2-Rep1_S35",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR3-Rep1_S83",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR4-Rep1_S89"
],
"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": "Measurement set [IGVFDS1261RWQY](/measurement-sets/IGVFDS1261RWQY/) 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/IGVFDS1261RWQY/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1261RWQY](/measurement-sets/IGVFDS1261RWQY/) has sequence file(s) [IGVFFI0052KUVQ](/sequence-files/IGVFFI0052KUVQ/), [IGVFFI4418OJED](/sequence-files/IGVFFI4418OJED/), [IGVFFI4610AVFG](/sequence-files/IGVFFI4610AVFG/), [IGVFFI3915XQVT](/sequence-files/IGVFFI3915XQVT/) 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/IGVFDS1261RWQY/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS6020CDHF](/auxiliary-sets/IGVFDS6020CDHF/) 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/IGVFDS6020CDHF/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9082URPW](/in-vitro-systems/IGVFSM9082URPW/) 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/IGVFSM9082URPW/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9082URPW](/in-vitro-systems/IGVFSM9082URPW/) 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/IGVFSM9082URPW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6020CDHF/",
"accession": "IGVFDS6020CDHF",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_SSFA2-Auxin6hrs-FF1"
],
"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": "2024-05-14T20:54:43.256583+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/IGVFFI8741XTAO/",
"accession": "IGVFFI8741XTAO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR2-Rep1_S35"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:09.077536+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI8741XTAO/@@download/IGVFFI8741XTAO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/82927251-3f0d-4dad-9c0d-99416a89784b/IGVFFI8741XTAO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinE-PCR2-Rep1_S35.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI0052KUVQ/",
"accession": "IGVFFI0052KUVQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR3-Rep1_S83"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:53.591925+00:00",
"file_format": "fastq",
"file_size": 22532638,
"href": "/sequence-files/IGVFFI0052KUVQ/@@download/IGVFFI0052KUVQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/88172735-9cf8-41a4-b299-bba6ecf58f02/IGVFFI0052KUVQ.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-BinE-PCR3-Rep1_S83_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4025OCGE/",
"accession": "IGVFFI4025OCGE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR1-Rep1_S29"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:53.515194+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI4025OCGE/@@download/IGVFFI4025OCGE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3c3f0caf-2ba0-4a8b-b8c0-1507a240f540/IGVFFI4025OCGE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinE-PCR1-Rep1_S29.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0337BOCJ/",
"accession": "IGVFFI0337BOCJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR3-Rep1_S83"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:24.170255+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI0337BOCJ/@@download/IGVFFI0337BOCJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b5b44404-3256-4ff8-a356-9eb99f6cd882/IGVFFI0337BOCJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinE-PCR3-Rep1_S83.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4418OJED/",
"accession": "IGVFFI4418OJED",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR4-Rep1_S89"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:12.263446+00:00",
"file_format": "fastq",
"file_size": 19839489,
"href": "/sequence-files/IGVFFI4418OJED/@@download/IGVFFI4418OJED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8cb54e16-a8b8-4cbc-88cb-de0b6dea9541/IGVFFI4418OJED.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-BinE-PCR4-Rep1_S89_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7209PXFH/",
"accession": "IGVFFI7209PXFH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR4-Rep1_S89"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:40.091006+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7209PXFH/@@download/IGVFFI7209PXFH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f7aa0dc6-749a-43ec-ae06-124aaa368c98/IGVFFI7209PXFH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinE-PCR4-Rep1_S89.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4610AVFG/",
"accession": "IGVFFI4610AVFG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR1-Rep1_S29"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:17.287935+00:00",
"file_format": "fastq",
"file_size": 16986806,
"href": "/sequence-files/IGVFFI4610AVFG/@@download/IGVFFI4610AVFG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5a8acc27-a743-4c20-adae-da692719600d/IGVFFI4610AVFG.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-BinE-PCR1-Rep1_S29_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3915XQVT/",
"accession": "IGVFFI3915XQVT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR2-Rep1_S35"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:35.378781+00:00",
"file_format": "fastq",
"file_size": 14005238,
"href": "/sequence-files/IGVFFI3915XQVT/@@download/IGVFFI3915XQVT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/caaf4a05-8e30-4b8d-bc2f-5ef2b147fbf2/IGVFFI3915XQVT.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-BinE-PCR2-Rep1_S35_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": "2024-07-10T19:52:31.150899+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9082URPW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9082URPW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR1-Rep1_S29",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR2-Rep1_S35",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR3-Rep1_S83",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinE-PCR4-Rep1_S89"
],
"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 E for 80-90% 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": "2024-06-01T01:47:17.287935+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": "f94bbd36-f814-4589-b13f-86cab3019eec"
}