{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2372JFBI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2372JFBI",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
],
"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/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3998EEZS](/in-vitro-systems/IGVFSM3998EEZS/) 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/IGVFSM3998EEZS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3998EEZS](/in-vitro-systems/IGVFSM3998EEZS/) 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/IGVFSM3998EEZS/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2372JFBI](/auxiliary-sets/IGVFDS2372JFBI/) has sequence file(s) [IGVFFI7923UEBL](/sequence-files/IGVFFI7923UEBL/), [IGVFFI7683TXPK](/sequence-files/IGVFFI7683TXPK/), [IGVFFI5849CCCH](/sequence-files/IGVFFI5849CCCH/), [IGVFFI3283FABB](/sequence-files/IGVFFI3283FABB/), [IGVFFI1366IKMD](/sequence-files/IGVFFI1366IKMD/), [IGVFFI1641ICFG](/sequence-files/IGVFFI1641ICFG/), [IGVFFI9101IEYD](/sequence-files/IGVFFI9101IEYD/), [IGVFFI3695WJWY](/sequence-files/IGVFFI3695WJWY/) 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/IGVFDS2372JFBI/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2372JFBI](/auxiliary-sets/IGVFDS2372JFBI/) 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/IGVFDS2372JFBI/"
}
]
},
"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": "2024-05-21T17:39:12.043233+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": "IGVFFI7923UEBL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:03:51.825076+00:00",
"file_format": "fastq",
"file_size": 23751591,
"href": "/sequence-files/IGVFFI7923UEBL/@@download/IGVFFI7923UEBL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a8655e69-0892-42ec-9ee7-4b2d0df07b1c/IGVFFI7923UEBL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1645SYMG/",
"accession": "IGVFFI1645SYMG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:33.443851+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI1645SYMG/@@download/IGVFFI1645SYMG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b8162409-6852-4207-be3f-16505cc03f34/IGVFFI1645SYMG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7683TXPK/",
"accession": "IGVFFI7683TXPK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:04:12.221861+00:00",
"file_format": "fastq",
"file_size": 25799470,
"href": "/sequence-files/IGVFFI7683TXPK/@@download/IGVFFI7683TXPK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/44decd1e-3d26-4e9f-9420-b05bd5f9c2c3/IGVFFI7683TXPK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinF-PCR1-Rep2_S171_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5849CCCH/",
"accession": "IGVFFI5849CCCH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:04:32.286509+00:00",
"file_format": "fastq",
"file_size": 31297415,
"href": "/sequence-files/IGVFFI5849CCCH/@@download/IGVFFI5849CCCH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/91a70b7a-e937-409a-87f1-054266735c23/IGVFFI5849CCCH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinF-PCR2-Rep1_S122_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3283FABB/",
"accession": "IGVFFI3283FABB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:05:12.698646+00:00",
"file_format": "fastq",
"file_size": 18205280,
"href": "/sequence-files/IGVFFI3283FABB/@@download/IGVFFI3283FABB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/538e5369-a3ba-435a-a874-9ffd7a7f3688/IGVFFI3283FABB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1366IKMD/",
"accession": "IGVFFI1366IKMD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:06:09.249109+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI1366IKMD/@@download/IGVFFI1366IKMD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/95bef792-53a5-4de7-8ec0-75896ac61d08/IGVFFI1366IKMD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1641ICFG/",
"accession": "IGVFFI1641ICFG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:04:52.822554+00:00",
"file_format": "fastq",
"file_size": 26259582,
"href": "/sequence-files/IGVFFI1641ICFG/@@download/IGVFFI1641ICFG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/19417ce7-bcb0-4381-9556-de92a2d0c776/IGVFFI1641ICFG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinF-PCR2-Rep2_S177_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9101IEYD/",
"accession": "IGVFFI9101IEYD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:05:31.718473+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI9101IEYD/@@download/IGVFFI9101IEYD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7465adf9-2c78-4049-86e6-9ee97d728bb4/IGVFFI9101IEYD.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2297PBGW/",
"accession": "IGVFFI2297PBGW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128"
],
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"creation_timestamp": "2024-06-11T20:50:32.562895+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2297PBGW/@@download/IGVFFI2297PBGW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4fe7a0ee-12fd-4709-9be0-8d5de997dc26/IGVFFI2297PBGW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3695WJWY/",
"accession": "IGVFFI3695WJWY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134"
],
"content_type": "reads",
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"href": "/sequence-files/IGVFFI3695WJWY/@@download/IGVFFI3695WJWY.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6743FDDQ/",
"accession": "IGVFFI6743FDDQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122"
],
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"creation_timestamp": "2024-06-11T20:50:03.255769+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI6743FDDQ/@@download/IGVFFI6743FDDQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b708b0a3-46ed-4fc2-aacb-8bd4f8c81d25/IGVFFI6743FDDQ.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9003PVUZ/",
"accession": "IGVFFI9003PVUZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:50:17.635560+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI9003PVUZ/@@download/IGVFFI9003PVUZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1245d430-9d0c-4e11-b060-915a8ffcde43/IGVFFI9003PVUZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1042MROS/",
"accession": "IGVFFI1042MROS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3921IQBX/",
"accession": "IGVFFI3921IQBX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134"
],
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"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI3921IQBX/@@download/IGVFFI3921IQBX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/339019be-322f-4003-a51b-5f0f602f6ca0/IGVFFI3921IQBX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3469LYTM/",
"accession": "IGVFFI3469LYTM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183"
],
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"href": "/configuration-files/IGVFFI3469LYTM/@@download/IGVFFI3469LYTM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f9af2208-4b14-4db6-ae9e-4f868390c510/IGVFFI3469LYTM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7439LMLL/",
"accession": "IGVFFI7439LMLL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:18.658071+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI7439LMLL/@@download/IGVFFI7439LMLL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/29871e62-f7cf-41b6-b706-8f47aef5387c/IGVFFI7439LMLL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6475UHMP/",
"accession": "IGVFDS6475UHMP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:21:24.755578+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3998EEZS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3998EEZS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep1_S116",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR1_Rep2_S171",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep1_S122",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR2_Rep2_S177",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep1_S128",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR3_Rep2_S183",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep1_S134",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinF-PCR4_Rep2_S189"
],
"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 F for 80-100% 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": "2024-06-01T02:03:51.825076+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "2e75aa19-c7b1-4773-bb78-d101c2bc4802"
}