{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6346MBBC/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6346MBBC",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep1_S136",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep1_S142",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep2_S197",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep1_S154",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9179ZLWQ](/in-vitro-systems/IGVFSM9179ZLWQ/) 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/IGVFSM9179ZLWQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9179ZLWQ](/in-vitro-systems/IGVFSM9179ZLWQ/) 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/IGVFSM9179ZLWQ/"
},
{
"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 [IGVFDS6346MBBC](/auxiliary-sets/IGVFDS6346MBBC/) has sequence file(s) [IGVFFI6733QFQU](/sequence-files/IGVFFI6733QFQU/), [IGVFFI4330WQPV](/sequence-files/IGVFFI4330WQPV/), [IGVFFI9912MXSK](/sequence-files/IGVFFI9912MXSK/), [IGVFFI0285SRTG](/sequence-files/IGVFFI0285SRTG/), [IGVFFI6507QLNG](/sequence-files/IGVFFI6507QLNG/), [IGVFFI9254WOTL](/sequence-files/IGVFFI9254WOTL/), [IGVFFI2079RGSD](/sequence-files/IGVFFI2079RGSD/), [IGVFFI2014UAIA](/sequence-files/IGVFFI2014UAIA/) 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/IGVFDS6346MBBC/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6346MBBC](/auxiliary-sets/IGVFDS6346MBBC/) 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/IGVFDS6346MBBC/"
}
]
},
"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": "2024-05-21T17:39:58.110587+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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{
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"accession": "IGVFFI6733QFQU",
"aliases": [
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],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 29550376,
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4885SSST/",
"accession": "IGVFFI4885SSST",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep1_S136"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:23.464240+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI4885SSST/@@download/IGVFFI4885SSST.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2809ad3c-d053-4984-9324-9941b1730421/IGVFFI4885SSST.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4330WQPV/",
"accession": "IGVFFI4330WQPV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:07:34.852493+00:00",
"file_format": "fastq",
"file_size": 15440567,
"href": "/sequence-files/IGVFFI4330WQPV/@@download/IGVFFI4330WQPV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/93ced886-2f1c-4b6a-b84b-1be9b93daa91/IGVFFI4330WQPV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinB-PCR3-Rep1_S148_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9912MXSK/",
"accession": "IGVFFI9912MXSK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 20070581,
"href": "/sequence-files/IGVFFI9912MXSK/@@download/IGVFFI9912MXSK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d9b48b5e-adf0-425a-ac60-47703df02e13/IGVFFI9912MXSK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinB-PCR3-Rep2_S203_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9412OHLV/",
"accession": "IGVFFI9412OHLV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:37.311149+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9412OHLV/@@download/IGVFFI9412OHLV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2f91c66e-5f98-443e-84aa-4cbe1418268a/IGVFFI9412OHLV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0285SRTG/",
"accession": "IGVFFI0285SRTG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191"
],
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"href": "/sequence-files/IGVFFI0285SRTG/@@download/IGVFFI0285SRTG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a223ede7-55c3-4c54-a448-b2f23787ba93/IGVFFI0285SRTG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6507QLNG/",
"accession": "IGVFFI6507QLNG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep1_S142"
],
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"creation_timestamp": "2024-06-01T02:06:57.278601+00:00",
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"s3_uri": "s3://igvf-files/2024/06/01/e8fbec48-cd84-4193-a390-8633588c5d21/IGVFFI6507QLNG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinB-PCR2-Rep1_S142_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9254WOTL/",
"accession": "IGVFFI9254WOTL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep2_S197"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2079RGSD/",
"accession": "IGVFFI2079RGSD",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2014UAIA/",
"accession": "IGVFFI2014UAIA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4783LAYC/",
"accession": "IGVFFI4783LAYC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191"
],
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"creation_timestamp": "2024-06-11T20:51:38.268506+00:00",
"file_format": "yaml",
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"s3_uri": "s3://igvf-files/2024/06/11/97df33a6-4ac9-421a-abc0-e60abedd5d55/IGVFFI4783LAYC.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9426DMVM/",
"accession": "IGVFFI9426DMVM",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:51.850784+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI9426DMVM/@@download/IGVFFI9426DMVM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d1bf782a-bce3-462a-8516-1dbd0d4f524b/IGVFFI9426DMVM.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1661FFXY/",
"accession": "IGVFFI1661FFXY",
"aliases": [
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],
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"href": "/configuration-files/IGVFFI1661FFXY/@@download/IGVFFI1661FFXY.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3568CAMJ/",
"accession": "IGVFFI3568CAMJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148"
],
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"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI3568CAMJ/@@download/IGVFFI3568CAMJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d05e0aac-dbcf-426c-8c25-13b3c6a91aef/IGVFFI3568CAMJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8534NOKY/",
"accession": "IGVFFI8534NOKY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep2_S197"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8897VNQR/",
"accession": "IGVFFI8897VNQR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209"
],
"content_type": "seqspec",
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"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI8897VNQR/@@download/IGVFFI8897VNQR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/aa2b03c6-50fa-4c23-9a72-59b3eef17fc4/IGVFFI8897VNQR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6690WAEP/",
"accession": "IGVFDS6690WAEP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep1_S136",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep1_S142",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep2_S197",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep1_S154",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:21:39.847404+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9179ZLWQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9179ZLWQ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep1_S136",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep1_S142",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep2_S197",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep1_S154",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209"
],
"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 B for 10-20% 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": "2024-06-01T02:06:15.587546+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a6ece6e8-60db-4f29-91e2-b13c1e3a6f7f"
}