{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8837KFKM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8837KFKM",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"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 related files",
"detail": "Measurement set [IGVFDS8837KFKM](/measurement-sets/IGVFDS8837KFKM/) has sequence file [IGVFFI6949YOXY](/sequence-files/IGVFFI6949YOXY/) which links to seqspec [IGVFFI1050EAZP](/configuration-files/IGVFFI1050EAZP/) which does not link to this file set. All files associated with a seqspec (both sequencing and seqspec files) are expected to be linked to the same file set.",
"level": 60,
"level_name": "ERROR",
"name": "audit_files_associated_with_incorrect_fileset",
"path": "/measurement-sets/IGVFDS8837KFKM/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8837KFKM](/measurement-sets/IGVFDS8837KFKM/) 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/IGVFDS8837KFKM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8837KFKM](/measurement-sets/IGVFDS8837KFKM/) has sequence file(s) [IGVFFI6949YOXY](/sequence-files/IGVFFI6949YOXY/), [IGVFFI3791DPCW](/sequence-files/IGVFFI3791DPCW/), [IGVFFI5485UKSW](/sequence-files/IGVFFI5485UKSW/), [IGVFFI9942MBPU](/sequence-files/IGVFFI9942MBPU/) 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/IGVFDS8837KFKM/"
},
{
"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 [IGVFSM5347ZNZW](/in-vitro-systems/IGVFSM5347ZNZW/) 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/IGVFSM5347ZNZW/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM5347ZNZW](/in-vitro-systems/IGVFSM5347ZNZW/) 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/IGVFSM5347ZNZW/"
}
]
},
"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": "2024-05-14T20:54:41.067986+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/IGVFFI5931KOIF/",
"accession": "IGVFFI5931KOIF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:48.321650+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5931KOIF/@@download/IGVFFI5931KOIF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0eed2e1a-98ea-40b1-baac-ff618c98f8a5/IGVFFI5931KOIF.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7432WZRT/",
"accession": "IGVFFI7432WZRT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:19.052656+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7432WZRT/@@download/IGVFFI7432WZRT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/17b39e58-60d3-4384-803c-b9cfc5b54b35/IGVFFI7432WZRT.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI9401XGMS/",
"accession": "IGVFFI9401XGMS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:34.488356+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9401XGMS/@@download/IGVFFI9401XGMS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/03555d92-92c9-4c50-8ab3-135216c62cd2/IGVFFI9401XGMS.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI6949YOXY/",
"accession": "IGVFFI6949YOXY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:29.366184+00:00",
"file_format": "fastq",
"file_size": 18518813,
"href": "/sequence-files/IGVFFI6949YOXY/@@download/IGVFFI6949YOXY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/25be7aca-554d-404b-8c42-d4e06789ff80/IGVFFI6949YOXY.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-BinC-PCR2-Rep1_S33_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3791DPCW/",
"accession": "IGVFFI3791DPCW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:47.588569+00:00",
"file_format": "fastq",
"file_size": 19766225,
"href": "/sequence-files/IGVFFI3791DPCW/@@download/IGVFFI3791DPCW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/971d1bd6-9b72-491e-b46e-8d4740ce15eb/IGVFFI3791DPCW.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-BinC-PCR3-Rep1_S81_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5485UKSW/",
"accession": "IGVFFI5485UKSW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:48:05.880288+00:00",
"file_format": "fastq",
"file_size": 23038811,
"href": "/sequence-files/IGVFFI5485UKSW/@@download/IGVFFI5485UKSW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ea709a3e-e5ca-40c8-9571-2228145c5dcd/IGVFFI5485UKSW.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-BinC-PCR4-Rep1_S87_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9942MBPU/",
"accession": "IGVFFI9942MBPU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:47:11.078698+00:00",
"file_format": "fastq",
"file_size": 15539789,
"href": "/sequence-files/IGVFFI9942MBPU/@@download/IGVFFI9942MBPU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e82c6741-d7a3-460d-bd76-c99a38072700/IGVFFI9942MBPU.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-BinC-PCR1-Rep1_S27_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": "2024-07-10T19:52:18.581411+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5347ZNZW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5347ZNZW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR1-Rep1_S27",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR2-Rep1_S33",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR3-Rep1_S81",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF1-BinC-PCR4-Rep1_S87"
],
"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": "2024-06-01T01:47:11.078698+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": "c9b78461-d0d6-451c-a178-031b6c68a8c8"
}