{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6061ICOS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6061ICOS",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR1-Rep1_S39",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR2-Rep1_S45",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR3-Rep1_S93",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR4-Rep1_S99"
],
"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 [IGVFSM2998MXSD](/in-vitro-systems/IGVFSM2998MXSD/) 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/IGVFSM2998MXSD/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6061ICOS](/measurement-sets/IGVFDS6061ICOS/) 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/IGVFDS6061ICOS/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6061ICOS](/measurement-sets/IGVFDS6061ICOS/) has sequence file(s) [IGVFFI2621UPCY](/sequence-files/IGVFFI2621UPCY/), [IGVFFI9523KYOD](/sequence-files/IGVFFI9523KYOD/), [IGVFFI9436BSSZ](/sequence-files/IGVFFI9436BSSZ/), [IGVFFI6368YITA](/sequence-files/IGVFFI6368YITA/) 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/IGVFDS6061ICOS/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2998MXSD](/in-vitro-systems/IGVFSM2998MXSD/) 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/IGVFSM2998MXSD/"
}
]
},
"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": "2024-05-14T20:55:10.106545+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/IGVFFI9860UXHH/",
"accession": "IGVFFI9860UXHH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR4-Rep1_S99"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:37.781654+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9860UXHH/@@download/IGVFFI9860UXHH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9181fd10-f61f-45d1-857c-476790d6ce33/IGVFFI9860UXHH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinC-PCR4-Rep1_S99.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7140HPIR/",
"accession": "IGVFFI7140HPIR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR2-Rep1_S45"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:06.628222+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI7140HPIR/@@download/IGVFFI7140HPIR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/70c3c7db-515d-4d25-988b-b2172e0dba9d/IGVFFI7140HPIR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinC-PCR2-Rep1_S45.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7261STXW/",
"accession": "IGVFFI7261STXW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR3-Rep1_S93"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:21.948708+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7261STXW/@@download/IGVFFI7261STXW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/01126284-b027-4704-8c97-50d3eefe965a/IGVFFI7261STXW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinC-PCR3-Rep1_S93.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2621UPCY/",
"accession": "IGVFFI2621UPCY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR3-Rep1_S93"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:59.198566+00:00",
"file_format": "fastq",
"file_size": 23584556,
"href": "/sequence-files/IGVFFI2621UPCY/@@download/IGVFFI2621UPCY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e367082f-e28b-4fb1-8f98-440534a954c4/IGVFFI2621UPCY.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-BinC-PCR3-Rep1_S93_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3081ZTTO/",
"accession": "IGVFFI3081ZTTO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR1-Rep1_S39"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:50.357446+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI3081ZTTO/@@download/IGVFFI3081ZTTO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9a2b404f-0090-4170-9465-150f3610f91f/IGVFFI3081ZTTO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinC-PCR1-Rep1_S39.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9523KYOD/",
"accession": "IGVFFI9523KYOD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR2-Rep1_S45"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:42.302723+00:00",
"file_format": "fastq",
"file_size": 1984226,
"href": "/sequence-files/IGVFFI9523KYOD/@@download/IGVFFI9523KYOD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5ff01b6d-5a9b-4cc2-9c89-8771e1a62bb2/IGVFFI9523KYOD.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-BinC-PCR2-Rep1_S45_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9436BSSZ/",
"accession": "IGVFFI9436BSSZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR1-Rep1_S39"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:24.392657+00:00",
"file_format": "fastq",
"file_size": 16560232,
"href": "/sequence-files/IGVFFI9436BSSZ/@@download/IGVFFI9436BSSZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3d5ea45f-9923-4ad6-835d-a7be599f30c0/IGVFFI9436BSSZ.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-BinC-PCR1-Rep1_S39_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6368YITA/",
"accession": "IGVFFI6368YITA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR4-Rep1_S99"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:49:18.253471+00:00",
"file_format": "fastq",
"file_size": 9895324,
"href": "/sequence-files/IGVFFI6368YITA/@@download/IGVFFI6368YITA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/31ed235a-97c9-45d6-89e0-eaa42ebbf513/IGVFFI6368YITA.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-BinC-PCR4-Rep1_S99_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": "2024-07-10T19:52:55.376388+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2998MXSD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2998MXSD",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR1-Rep1_S39",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR2-Rep1_S45",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR3-Rep1_S93",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinC-PCR4-Rep1_S99"
],
"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 C for 35-45% 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": "2024-06-01T01:48:24.392657+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": "c422ea5b-b047-4087-8485-f2d7634ba398"
}