{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9728LNRU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9728LNRU",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep1_S111",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep2_S166",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep1_S117",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep2_S172",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR3_Rep1_S123",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR3_Rep2_S178",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep1_S129",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep2_S184"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3056RYCY](/in-vitro-systems/IGVFSM3056RYCY/) 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/IGVFSM3056RYCY/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3056RYCY](/in-vitro-systems/IGVFSM3056RYCY/) 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/IGVFSM3056RYCY/"
},
{
"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 [IGVFDS9728LNRU](/auxiliary-sets/IGVFDS9728LNRU/) has sequence file(s) [IGVFFI5075LZIL](/sequence-files/IGVFFI5075LZIL/), [IGVFFI9039RXBK](/sequence-files/IGVFFI9039RXBK/), [IGVFFI3563HVLI](/sequence-files/IGVFFI3563HVLI/), [IGVFFI2814SFWJ](/sequence-files/IGVFFI2814SFWJ/), [IGVFFI2985VSGE](/sequence-files/IGVFFI2985VSGE/), [IGVFFI7757VRPV](/sequence-files/IGVFFI7757VRPV/), [IGVFFI2289LZDO](/sequence-files/IGVFFI2289LZDO/), [IGVFFI8727LXUE](/sequence-files/IGVFFI8727LXUE/) 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/IGVFDS9728LNRU/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9728LNRU](/auxiliary-sets/IGVFDS9728LNRU/) 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/IGVFDS9728LNRU/"
}
]
},
"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": "2024-05-21T17:39:05.286626+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": "IGVFFI5075LZIL",
"aliases": [
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4492TGXP/",
"accession": "IGVFFI4492TGXP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep1_S111"
],
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"creation_timestamp": "2024-06-11T20:49:20.902143+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI4492TGXP/@@download/IGVFFI4492TGXP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/38c0812c-8a82-4c9c-9228-309afa49488f/IGVFFI4492TGXP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinA-PCR1_Rep1_S111.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9039RXBK/",
"accession": "IGVFFI9039RXBK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep2_S166"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:03:55.093307+00:00",
"file_format": "fastq",
"file_size": 25923298,
"href": "/sequence-files/IGVFFI9039RXBK/@@download/IGVFFI9039RXBK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5681d9d5-5614-49f6-8e1d-6b0d614ca272/IGVFFI9039RXBK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinA-PCR1-Rep2_S166_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3563HVLI/",
"accession": "IGVFFI3563HVLI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep2_S172"
],
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"href": "/sequence-files/IGVFFI3563HVLI/@@download/IGVFFI3563HVLI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/37e8bbaf-bff1-4a6e-8cc3-810a4f5b6398/IGVFFI3563HVLI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF1-BinA-PCR2-Rep2_S172_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2814SFWJ/",
"accession": "IGVFFI2814SFWJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep2_S184"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:05:53.312070+00:00",
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"href": "/sequence-files/IGVFFI2814SFWJ/@@download/IGVFFI2814SFWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f07a5a48-6608-4996-a15f-0c7816ec5a9b/IGVFFI2814SFWJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9696GNVY/",
"accession": "IGVFFI9696GNVY",
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],
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"href": "/configuration-files/IGVFFI9696GNVY/@@download/IGVFFI9696GNVY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/16b59842-5b12-4467-b04d-103cf5877cc6/IGVFFI9696GNVY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinA-PCR2_Rep2_S172.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3540RMKW/",
"accession": "IGVFFI3540RMKW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR3_Rep1_S123"
],
"content_type": "seqspec",
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI3540RMKW/@@download/IGVFFI3540RMKW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2644eb3f-f700-4f26-9b31-3dc63808901e/IGVFFI3540RMKW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinA-PCR3_Rep1_S123.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8520ASYZ/",
"accession": "IGVFFI8520ASYZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep1_S129"
],
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"href": "/configuration-files/IGVFFI8520ASYZ/@@download/IGVFFI8520ASYZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/29ecfba9-0f25-4ffa-b1a1-26f36759d0e3/IGVFFI8520ASYZ.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2985VSGE/",
"accession": "IGVFFI2985VSGE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep1_S117"
],
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"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7757VRPV/",
"accession": "IGVFFI7757VRPV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep1_S129"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:05:34.600953+00:00",
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"href": "/sequence-files/IGVFFI7757VRPV/@@download/IGVFFI7757VRPV.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2289LZDO/",
"accession": "IGVFFI2289LZDO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR3_Rep1_S123"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8727LXUE/",
"accession": "IGVFFI8727LXUE",
"aliases": [
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],
"content_type": "reads",
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"file_format": "fastq",
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"href": "/sequence-files/IGVFFI8727LXUE/@@download/IGVFFI8727LXUE.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0706VNBX/",
"accession": "IGVFFI0706VNBX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep2_S166"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9950ZGFX/",
"accession": "IGVFFI9950ZGFX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep1_S117"
],
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"file_size": 911,
"href": "/configuration-files/IGVFFI9950ZGFX/@@download/IGVFFI9950ZGFX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3cfd845a-c1f2-4494-8fec-d75ced5f1402/IGVFFI9950ZGFX.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9250ZNHJ/",
"accession": "IGVFFI9250ZNHJ",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5421EMLL/",
"accession": "IGVFFI5421EMLL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep2_S184"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:06.039760+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5421EMLL/@@download/IGVFFI5421EMLL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a45824f1-eaf9-4ea8-9a93-af99f63d677b/IGVFFI5421EMLL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF1-BinA-PCR4_Rep2_S184.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7182DGDS/",
"accession": "IGVFDS7182DGDS",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep1_S111",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep2_S166",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep1_S117",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep2_S172",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR3_Rep1_S123",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR3_Rep2_S178",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep1_S129",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep2_S184"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:20:47.096634+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3056RYCY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3056RYCY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep1_S111",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR1_Rep2_S166",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep1_S117",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR2_Rep2_S172",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR3_Rep1_S123",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR3_Rep2_S178",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep1_S129",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF1-BinA-PCR4_Rep2_S184"
],
"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": "2024-06-01T02:03:35.207316+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ed08e466-99f5-4449-9acb-815b1f78b529"
}