{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1298BFAZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
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"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep2_S56",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep1_S7",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep1_S13",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep1_S19",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep2_S74"
],
"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": "In vitro system [IGVFSM3086DQMC](/in-vitro-systems/IGVFSM3086DQMC/) 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/IGVFSM3086DQMC/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS5951VSHM](/auxiliary-sets/IGVFDS5951VSHM/) 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/IGVFDS5951VSHM/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1298BFAZ](/measurement-sets/IGVFDS1298BFAZ/) 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/IGVFDS1298BFAZ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1298BFAZ](/measurement-sets/IGVFDS1298BFAZ/) has sequence file(s) [IGVFFI7230YSEB](/sequence-files/IGVFFI7230YSEB/), [IGVFFI5243KTWV](/sequence-files/IGVFFI5243KTWV/), [IGVFFI5803HMJL](/sequence-files/IGVFFI5803HMJL/), [IGVFFI8079GYLE](/sequence-files/IGVFFI8079GYLE/), [IGVFFI8310ZXDQ](/sequence-files/IGVFFI8310ZXDQ/), [IGVFFI1423QMWB](/sequence-files/IGVFFI1423QMWB/), [IGVFFI7962MDES](/sequence-files/IGVFFI7962MDES/), [IGVFFI9473RAYZ](/sequence-files/IGVFFI9473RAYZ/) 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/IGVFDS1298BFAZ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM3086DQMC](/in-vitro-systems/IGVFSM3086DQMC/) 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/IGVFSM3086DQMC/"
}
]
},
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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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}
],
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}
],
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],
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],
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{
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],
"sex": "male",
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}
],
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},
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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-Auxin0hrs-FF1-BinA-PCR4-Rep1_S19_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9473RAYZ/",
"accession": "IGVFFI9473RAYZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:59:42.089432+00:00",
"file_format": "fastq",
"file_size": 22662868,
"href": "/sequence-files/IGVFFI9473RAYZ/@@download/IGVFFI9473RAYZ.fastq.gz",
"md5sum": "d52e83996c902f2cd81e626afa80af83",
"s3_uri": "s3://igvf-files/2024/06/01/60d1cb10-f76d-427b-b42a-1af6c356d185/IGVFFI9473RAYZ.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-Auxin0hrs-FF1-BinA-PCR3-Rep2_S68_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": "2024-07-10T19:46:16.243123+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3086DQMC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3086DQMC",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep2_S56",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep1_S7",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep1_S13",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep1_S19",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep2_S74"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"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 A for 0-10% expression of MYC) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:58:01.097868+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": "f64a8b0f-1c14-4e13-92af-a915aa8c8f7d"
}