{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3773NYHJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3773NYHJ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep1_S135",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep2_S196",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep1_S147",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9689GGGO](/in-vitro-systems/IGVFSM9689GGGO/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9689GGGO/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9689GGGO](/in-vitro-systems/IGVFSM9689GGGO/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9689GGGO/"
},
{
"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 sequencing kit",
"detail": "Auxiliary set [IGVFDS3773NYHJ](/auxiliary-sets/IGVFDS3773NYHJ/) has sequence file(s) [IGVFFI0625IJAQ](/sequence-files/IGVFFI0625IJAQ/), [IGVFFI9925PDQT](/sequence-files/IGVFFI9925PDQT/), [IGVFFI5272TWLQ](/sequence-files/IGVFFI5272TWLQ/), [IGVFFI1923OXRY](/sequence-files/IGVFFI1923OXRY/), [IGVFFI2912HULO](/sequence-files/IGVFFI2912HULO/), [IGVFFI7847XCEY](/sequence-files/IGVFFI7847XCEY/), [IGVFFI0779HVAM](/sequence-files/IGVFFI0779HVAM/), [IGVFFI7772BVHA](/sequence-files/IGVFFI7772BVHA/) 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/IGVFDS3773NYHJ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3773NYHJ](/auxiliary-sets/IGVFDS3773NYHJ/) 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/IGVFDS3773NYHJ/"
}
]
},
"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": "2024-05-21T17:39:57.275820+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"accession": "IGVFFI0625IJAQ",
"aliases": [
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],
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"file_format": "fastq",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9113KRZX/",
"accession": "IGVFFI9113KRZX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep1_S135"
],
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"creation_timestamp": "2024-06-11T20:51:21.162933+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI9113KRZX/@@download/IGVFFI9113KRZX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/67b413ec-9873-4f27-83ff-1d280d40f250/IGVFFI9113KRZX.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9925PDQT/",
"accession": "IGVFFI9925PDQT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:06:54.003981+00:00",
"file_format": "fastq",
"file_size": 24568124,
"href": "/sequence-files/IGVFFI9925PDQT/@@download/IGVFFI9925PDQT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1f543a4a-82f9-46ff-92a8-db410f3561bc/IGVFFI9925PDQT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinA-PCR2-Rep1_S141_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6092JPSK/",
"accession": "IGVFFI6092JPSK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141"
],
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"href": "/configuration-files/IGVFFI6092JPSK/@@download/IGVFFI6092JPSK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/efb548ef-0cec-48d7-b9ff-bdcdc7fe9d13/IGVFFI6092JPSK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5272TWLQ/",
"accession": "IGVFFI5272TWLQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:06:34.291404+00:00",
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"s3_uri": "s3://igvf-files/2024/06/01/56666d9c-c3a3-437a-8954-77a5f6125169/IGVFFI5272TWLQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1923OXRY/",
"accession": "IGVFFI1923OXRY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
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"s3_uri": "s3://igvf-files/2024/06/01/53748a81-3d3c-4713-98df-c5f66b76659c/IGVFFI1923OXRY.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2912HULO/",
"accession": "IGVFFI2912HULO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep1_S147"
],
"content_type": "reads",
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"s3_uri": "s3://igvf-files/2024/06/01/702ff99c-9e47-4b2a-860f-f3aba6fdb5e3/IGVFFI2912HULO.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0240BUEF/",
"accession": "IGVFFI0240BUEF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153"
],
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"href": "/configuration-files/IGVFFI0240BUEF/@@download/IGVFFI0240BUEF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/52a169cc-bc6e-4c4d-8da1-b9159454aa4c/IGVFFI0240BUEF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7847XCEY/",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0779HVAM/",
"accession": "IGVFFI0779HVAM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7772BVHA/",
"accession": "IGVFFI7772BVHA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8212FHGM/",
"accession": "IGVFFI8212FHGM",
"aliases": [
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],
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"href": "/configuration-files/IGVFFI8212FHGM/@@download/IGVFFI8212FHGM.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8226ETLT/",
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"aliases": [
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],
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},
{
"@id": "/configuration-files/IGVFFI1780ZMBE/",
"accession": "IGVFFI1780ZMBE",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190"
],
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"href": "/configuration-files/IGVFFI1780ZMBE/@@download/IGVFFI1780ZMBE.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6953RQCU/",
"accession": "IGVFFI6953RQCU",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1138TVPD/",
"accession": "IGVFFI1138TVPD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
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"s3_uri": "s3://igvf-files/2024/06/11/e3925461-b372-44d9-bae7-eeb688875a19/IGVFFI1138TVPD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9717YXWE/",
"accession": "IGVFDS9717YXWE",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep1_S135",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep2_S196",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep1_S147",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:21:32.218942+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9689GGGO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9689GGGO",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep1_S135",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR1_Rep2_S190",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep1_S141",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR2_Rep2_S196",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep1_S147",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep1_S153",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR4_Rep2_S208"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
"/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"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) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:06:12.280802+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "34ceeb44-77f1-4761-be4d-3535d706f4fc"
}