{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2690TTFH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2690TTFH",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"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 [IGVFDS9055BZJI](/auxiliary-sets/IGVFDS9055BZJI/) 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/IGVFDS9055BZJI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0373CYTT](/in-vitro-systems/IGVFSM0373CYTT/) 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/IGVFSM0373CYTT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2690TTFH](/measurement-sets/IGVFDS2690TTFH/) 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/IGVFDS2690TTFH/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2690TTFH](/measurement-sets/IGVFDS2690TTFH/) has sequence file(s) [IGVFFI4677UICJ](/sequence-files/IGVFFI4677UICJ/), [IGVFFI1400XMFH](/sequence-files/IGVFFI1400XMFH/), [IGVFFI4501LVHP](/sequence-files/IGVFFI4501LVHP/), [IGVFFI1659OMPY](/sequence-files/IGVFFI1659OMPY/), [IGVFFI5888TLGJ](/sequence-files/IGVFFI5888TLGJ/), [IGVFFI1838TDNU](/sequence-files/IGVFFI1838TDNU/), [IGVFFI6767UOHJ](/sequence-files/IGVFFI6767UOHJ/), [IGVFFI7202ZYZL](/sequence-files/IGVFFI7202ZYZL/) 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/IGVFDS2690TTFH/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM0373CYTT](/in-vitro-systems/IGVFSM0373CYTT/) 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/IGVFSM0373CYTT/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9055BZJI/",
"accession": "IGVFDS9055BZJI",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_MYC-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"
},
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{
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"accession": "IGVFDS7857SYCK",
"file_set_type": "guide library",
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{
"@id": "/tabular-files/IGVFFI3782KCTX/",
"accession": "IGVFFI3782KCTX",
"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": "2024-05-21T17:34:59.620731+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": [
{
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"accession": "IGVFFI3679ETJZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:28.629750+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI3679ETJZ/@@download/IGVFFI3679ETJZ.yaml.gz",
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"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7989FMBQ/",
"accession": "IGVFFI7989FMBQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:58.282008+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI7989FMBQ/@@download/IGVFFI7989FMBQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a017b58e-0227-4c00-bd6d-12edb5694df3/IGVFFI7989FMBQ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI5910EETS/",
"accession": "IGVFFI5910EETS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:42.397852+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5910EETS/@@download/IGVFFI5910EETS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f8588a9b-e786-4530-aff8-40fc96b7d2c3/IGVFFI5910EETS.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI7948HLPP/",
"accession": "IGVFFI7948HLPP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:13.703174+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI7948HLPP/@@download/IGVFFI7948HLPP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c6c9cf0e-eea8-40e2-aa63-d0cf384b4081/IGVFFI7948HLPP.yaml.gz",
"status": "released",
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"upload_status": "validation exempted"
},
{
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],
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"creation_timestamp": "2024-06-11T20:49:43.425654+00:00",
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"href": "/configuration-files/IGVFFI4121BJCJ/@@download/IGVFFI4121BJCJ.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1455JJRV/",
"accession": "IGVFFI1455JJRV",
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],
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"creation_timestamp": "2024-06-11T20:50:12.928467+00:00",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2204VYTD/",
"accession": "IGVFFI2204VYTD",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:57.786455+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2204VYTD/@@download/IGVFFI2204VYTD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5cd253b1-9235-4b1a-8994-44c80972a8d1/IGVFFI2204VYTD.yaml.gz",
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},
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],
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"href": "/configuration-files/IGVFFI2455NBTS/@@download/IGVFFI2455NBTS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1d9b001f-0717-4c4f-8df1-6550b7fad6fe/IGVFFI2455NBTS.yaml.gz",
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},
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],
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},
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},
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},
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},
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},
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},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinD-PCR3-Rep2_S181_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"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": "2024-07-10T19:48:01.360046+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0373CYTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0373CYTT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep1_S114",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR1_Rep2_S169",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep1_S120",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR2_Rep2_S175",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep1_S126",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR3_Rep2_S181",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep1_S132",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinD-PCR4_Rep2_S187"
],
"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 MYC) 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": "2024-06-01T02:03:45.203043+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of MYC integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000136997/",
"geneid": "ENSG00000136997",
"name": "MYC proto-oncogene, bHLH transcription factor",
"status": "released",
"symbol": "MYC",
"synonyms": [
"bHLHe39",
"myc-related translation/localization regulatory factor",
"MYC proto-oncogene, bHLH transcription factor",
"MYC",
"c-Myc",
"v-myc avian myelocytomatosis viral oncogene homolog",
"proto-oncogene c-Myc",
"transcription factor p64",
"myc proto-oncogene protein",
"avian myelocytomatosis viral oncogene homolog",
"MRTL",
"class E basic helix-loop-helix protein 39",
"MYCC",
"v-myc myelocytomatosis viral oncogene homolog"
]
}
],
"uuid": "2054038e-8d83-4442-af43-bf9a70e30042"
}