{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6736VYAD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6736VYAD",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR1_Rep1_S113",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR1_Rep2_S168",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR2_Rep1_S119",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR2_Rep2_S174",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR3_Rep1_S125",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR3_Rep2_S180",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR4_Rep1_S131",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR4_Rep2_S186"
],
"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 [IGVFDS6736VYAD](/measurement-sets/IGVFDS6736VYAD/) 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/IGVFDS6736VYAD/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6736VYAD](/measurement-sets/IGVFDS6736VYAD/) has sequence file(s) [IGVFFI4955BTQI](/sequence-files/IGVFFI4955BTQI/), [IGVFFI2400OIYG](/sequence-files/IGVFFI2400OIYG/), [IGVFFI3236EOMO](/sequence-files/IGVFFI3236EOMO/), [IGVFFI8078ZIFD](/sequence-files/IGVFFI8078ZIFD/), [IGVFFI3855ICMO](/sequence-files/IGVFFI3855ICMO/), [IGVFFI6439DTIW](/sequence-files/IGVFFI6439DTIW/), [IGVFFI9411SKQQ](/sequence-files/IGVFFI9411SKQQ/), [IGVFFI4270WMJY](/sequence-files/IGVFFI4270WMJY/) 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/IGVFDS6736VYAD/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3296OBHK](/in-vitro-systems/IGVFSM3296OBHK/) 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/IGVFSM3296OBHK/"
},
{
"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/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3296OBHK](/in-vitro-systems/IGVFSM3296OBHK/) 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/IGVFSM3296OBHK/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7857SYCK/",
"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": "2024-05-21T17:34:58.193183+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": "IGVFFI2456ADVB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR4_Rep1_S131"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:54.709529+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2456ADVB/@@download/IGVFFI2456ADVB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b211766c-393a-4647-8d37-e14099379247/IGVFFI2456ADVB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinC-PCR4_Rep1_S131.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4955BTQI/",
"accession": "IGVFFI4955BTQI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR4_Rep2_S186"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:05:59.520176+00:00",
"file_format": "fastq",
"file_size": 23622351,
"href": "/sequence-files/IGVFFI4955BTQI/@@download/IGVFFI4955BTQI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7b604b43-1b7e-462f-89a2-407f89a4064b/IGVFFI4955BTQI.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinC-PCR4-Rep2_S186_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1389JGYH/",
"accession": "IGVFFI1389JGYH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR2_Rep2_S174"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:10.409837+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI1389JGYH/@@download/IGVFFI1389JGYH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0d210ac9-7889-4e4b-9960-cb6e3f64bdd7/IGVFFI1389JGYH.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinC-PCR2_Rep2_S174.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3574SVFD/",
"accession": "IGVFFI3574SVFD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR4_Rep2_S186"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:11.264947+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI3574SVFD/@@download/IGVFFI3574SVFD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6b4de511-df30-45aa-99b6-fb2b994c7aae/IGVFFI3574SVFD.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinC-PCR4_Rep2_S186.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3511CDMV/",
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"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR1_Rep1_S113"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:26.217195+00:00",
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"file_size": 911,
"href": "/configuration-files/IGVFFI3511CDMV/@@download/IGVFFI3511CDMV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e7e0d204-1c2a-4176-9e4e-21c58a28e4c5/IGVFFI3511CDMV.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI2400OIYG/",
"accession": "IGVFFI2400OIYG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR2_Rep1_S119"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:04:22.078630+00:00",
"file_format": "fastq",
"file_size": 27624846,
"href": "/sequence-files/IGVFFI2400OIYG/@@download/IGVFFI2400OIYG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d96352ec-3e46-432d-8a14-c8b2f1242fac/IGVFFI2400OIYG.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinC-PCR2-Rep1_S119_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6918QVQL/",
"accession": "IGVFFI6918QVQL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR2_Rep1_S119"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:55.613366+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6918QVQL/@@download/IGVFFI6918QVQL.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4106TIWV/",
"accession": "IGVFFI4106TIWV",
"aliases": [
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],
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"creation_timestamp": "2024-06-11T20:50:25.268591+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4106TIWV/@@download/IGVFFI4106TIWV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4f92da19-9ca6-4436-8fcd-a57ae333bd8e/IGVFFI4106TIWV.yaml.gz",
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"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3236EOMO/",
"accession": "IGVFFI3236EOMO",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-06-01T02:04:42.871242+00:00",
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"file_size": 22383603,
"href": "/sequence-files/IGVFFI3236EOMO/@@download/IGVFFI3236EOMO.fastq.gz",
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"upload_status": "validated"
},
{
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"aliases": [
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],
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"href": "/configuration-files/IGVFFI5226BOFH/@@download/IGVFFI5226BOFH.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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},
{
"@id": "/sequence-files/IGVFFI9411SKQQ/",
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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-BinC-PCR3-Rep1_S125_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": "2024-07-10T19:47:53.549253+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3296OBHK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3296OBHK",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR1_Rep1_S113",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR1_Rep2_S168",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR2_Rep1_S119",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR2_Rep2_S174",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR3_Rep1_S125",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR3_Rep2_S180",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR4_Rep1_S131",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinC-PCR4_Rep2_S186"
],
"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 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": "2024-06-01T02:03:41.823464+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": "13cbcf42-9327-4b70-b0e7-2c902b0ec611"
}