{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1298BFAZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1298BFAZ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1",
"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/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5951VSHM](/auxiliary-sets/IGVFDS5951VSHM/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS5951VSHM/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2805FQAD](/auxiliary-sets/IGVFDS2805FQAD/) has sequence file(s) [IGVFFI8310ZXDQ](/sequence-files/IGVFFI8310ZXDQ/), [IGVFFI9473RAYZ](/sequence-files/IGVFFI9473RAYZ/), [IGVFFI7962MDES](/sequence-files/IGVFFI7962MDES/), [IGVFFI1423QMWB](/sequence-files/IGVFFI1423QMWB/), [IGVFFI7230YSEB](/sequence-files/IGVFFI7230YSEB/), [IGVFFI5243KTWV](/sequence-files/IGVFFI5243KTWV/), [IGVFFI8079GYLE](/sequence-files/IGVFFI8079GYLE/), [IGVFFI5803HMJL](/sequence-files/IGVFFI5803HMJL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS2805FQAD/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2805FQAD](/auxiliary-sets/IGVFDS2805FQAD/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS2805FQAD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5951VSHM/",
"accession": "IGVFDS5951VSHM",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_MYC-Auxin0hrs-FF1"
],
"file_set_type": "cell sorting"
},
{
"@id": "/auxiliary-sets/IGVFDS2805FQAD/",
"accession": "IGVFDS2805FQAD",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep2_S56",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep1_S7",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep1_S13",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep1_S19",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep2_S74"
],
"file_set_type": "gRNA sequencing"
}
],
"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"
},
"control_for": [],
"creation_timestamp": "2024-05-21T17:15:12.925528+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"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [],
"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"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7857SYCK/",
"accession": "IGVFDS7857SYCK",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of MYC) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"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": "CRISPR interference FlowFISH screen 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",
"symbol": "MYC",
"synonyms": [
"bHLHe39",
"v-myc myelocytomatosis viral oncogene homolog",
"myc proto-oncogene protein",
"avian myelocytomatosis viral oncogene homolog",
"v-myc avian myelocytomatosis viral oncogene homolog",
"transcription factor p64",
"MRTL",
"c-Myc",
"myc-related translation/localization regulatory factor",
"MYCC",
"class E basic helix-loop-helix protein 39",
"proto-oncogene c-Myc"
]
}
],
"uuid": "f64a8b0f-1c14-4e13-92af-a915aa8c8f7d"
}