{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1564ZVKC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1564ZVKC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep1_S140",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep2_S195",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep1_S146",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep2_S201",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep1_S152",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep2_S207",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep1_S158",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213"
],
"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 [IGVFDS1564ZVKC](/measurement-sets/IGVFDS1564ZVKC/) 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/IGVFDS1564ZVKC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1564ZVKC](/measurement-sets/IGVFDS1564ZVKC/) has sequence file(s) [IGVFFI4207NYCN](/sequence-files/IGVFFI4207NYCN/), [IGVFFI9220ZDKH](/sequence-files/IGVFFI9220ZDKH/), [IGVFFI9861RLTL](/sequence-files/IGVFFI9861RLTL/), [IGVFFI6772UIRN](/sequence-files/IGVFFI6772UIRN/), [IGVFFI6947RKEO](/sequence-files/IGVFFI6947RKEO/), [IGVFFI4385VBWZ](/sequence-files/IGVFFI4385VBWZ/), [IGVFFI5709RWIZ](/sequence-files/IGVFFI5709RWIZ/), [IGVFFI2502UDBL](/sequence-files/IGVFFI2502UDBL/) 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/IGVFDS1564ZVKC/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS5394TNHK](/auxiliary-sets/IGVFDS5394TNHK/) 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/IGVFDS5394TNHK/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3012RMVA](/in-vitro-systems/IGVFSM3012RMVA/) 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/IGVFSM3012RMVA/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3012RMVA](/in-vitro-systems/IGVFSM3012RMVA/) 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/IGVFSM3012RMVA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5394TNHK/",
"accession": "IGVFDS5394TNHK",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_MYC-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": [
{
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"accession": "IGVFDS7857SYCK",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@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": "2024-05-21T17:36:00.992860+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": "IGVFFI5460AWQH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:53:16.211077+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5460AWQH/@@download/IGVFFI5460AWQH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/899ce2cf-7678-4489-a6ab-22cf1ba65188/IGVFFI5460AWQH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0457OIVE/",
"accession": "IGVFFI0457OIVE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep2_S195"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:48.193263+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0457OIVE/@@download/IGVFFI0457OIVE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/075ddeb3-1afd-4e28-b192-8654ff13c525/IGVFFI0457OIVE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinF-PCR1_Rep2_S195.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4158BVCP/",
"accession": "IGVFFI4158BVCP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep2_S207"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:47.041551+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4158BVCP/@@download/IGVFFI4158BVCP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/65b91d6d-dbfc-45ed-9f02-31d84cc4e6d7/IGVFFI4158BVCP.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinF-PCR3_Rep2_S207.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2568FNBM/",
"accession": "IGVFFI2568FNBM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep1_S152"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:32.490947+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2568FNBM/@@download/IGVFFI2568FNBM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/88b9c789-6255-4fb9-b852-f225418408ad/IGVFFI2568FNBM.yaml.gz",
"status": "released",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI2148WQLI/",
"accession": "IGVFFI2148WQLI",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:03.235995+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2148WQLI/@@download/IGVFFI2148WQLI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cc8c31cd-e5d0-4717-a8f3-3d5070474d8b/IGVFFI2148WQLI.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1727DFOC/",
"accession": "IGVFFI1727DFOC",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:17.842895+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1727DFOC/@@download/IGVFFI1727DFOC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7ad1e1d7-df94-4350-9022-260fd9101186/IGVFFI1727DFOC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinF-PCR2_Rep2_S201.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4653RFBA/",
"accession": "IGVFFI4653RFBA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep1_S140"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:33.275649+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4653RFBA/@@download/IGVFFI4653RFBA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e2154c23-4aff-4382-b92f-753134cf9778/IGVFFI4653RFBA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinF-PCR1_Rep1_S140.yaml",
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},
{
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"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-06-01T02:08:24.763839+00:00",
"file_format": "fastq",
"file_size": 25459713,
"href": "/sequence-files/IGVFFI4207NYCN/@@download/IGVFFI4207NYCN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/807e3677-97f5-4048-bb74-072c0a5e8c7f/IGVFFI4207NYCN.fastq.gz",
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"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinF-PCR4-Rep1_S158_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9220ZDKH/",
"accession": "IGVFFI9220ZDKH",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-06-01T02:08:06.259129+00:00",
"file_format": "fastq",
"file_size": 28490577,
"href": "/sequence-files/IGVFFI9220ZDKH/@@download/IGVFFI9220ZDKH.fastq.gz",
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},
{
"@id": "/configuration-files/IGVFFI3737AKUY/",
"accession": "IGVFFI3737AKUY",
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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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"upload_status": "validated"
},
{
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],
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},
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"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinF-PCR3-Rep1_S152_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": "2024-07-10T19:49:05.254691+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3012RMVA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3012RMVA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep1_S140",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR1_Rep2_S195",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep1_S146",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR2_Rep2_S201",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep1_S152",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR3_Rep2_S207",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep1_S158",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinF-PCR4_Rep2_S213"
],
"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 F for 80-100% 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": "2024-06-01T02:06:31.321958+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": "f9389ff1-8452-43ea-a522-a576ab5fbe9e"
}