{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1748WPZO/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1748WPZO",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep1_S139",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep1_S145",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep2_S200",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep1_S157",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212"
],
"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 [IGVFSM2548FJWP](/in-vitro-systems/IGVFSM2548FJWP/) 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/IGVFSM2548FJWP/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2548FJWP](/in-vitro-systems/IGVFSM2548FJWP/) 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/IGVFSM2548FJWP/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1748WPZO](/auxiliary-sets/IGVFDS1748WPZO/) has sequence file(s) [IGVFFI7918JLEC](/sequence-files/IGVFFI7918JLEC/), [IGVFFI4124LZQS](/sequence-files/IGVFFI4124LZQS/), [IGVFFI1556PTKF](/sequence-files/IGVFFI1556PTKF/), [IGVFFI6201YBUU](/sequence-files/IGVFFI6201YBUU/), [IGVFFI0138SEGI](/sequence-files/IGVFFI0138SEGI/), [IGVFFI7692ITME](/sequence-files/IGVFFI7692ITME/), [IGVFFI7499BCPY](/sequence-files/IGVFFI7499BCPY/), [IGVFFI4194ZWJO](/sequence-files/IGVFFI4194ZWJO/) 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/IGVFDS1748WPZO/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1748WPZO](/auxiliary-sets/IGVFDS1748WPZO/) 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/IGVFDS1748WPZO/"
}
]
},
"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": "2024-05-21T17:40:00.726262+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": "IGVFFI7918JLEC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep1_S139"
],
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"file_format": "fastq",
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"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3429AKQI/",
"accession": "IGVFFI3429AKQI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep1_S139"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:30.809871+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI3429AKQI/@@download/IGVFFI3429AKQI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2cd609ef-c6aa-43a8-83cf-7c3d700dc0fa/IGVFFI3429AKQI.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4124LZQS/",
"accession": "IGVFFI4124LZQS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep1_S157"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:08:21.773960+00:00",
"file_format": "fastq",
"file_size": 21887613,
"href": "/sequence-files/IGVFFI4124LZQS/@@download/IGVFFI4124LZQS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/212f976c-9129-463b-8022-28085910d8c6/IGVFFI4124LZQS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinE-PCR4-Rep1_S157_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1556PTKF/",
"accession": "IGVFFI1556PTKF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212"
],
"content_type": "reads",
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"href": "/sequence-files/IGVFFI1556PTKF/@@download/IGVFFI1556PTKF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2c88b652-a3bd-48ed-b9a6-c9924ac4dae5/IGVFFI1556PTKF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinE-PCR4-Rep2_S212_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2553TBGP/",
"accession": "IGVFFI2553TBGP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:45.731784+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2553TBGP/@@download/IGVFFI2553TBGP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a5708691-359f-491a-bb9f-d67f31ebb66f/IGVFFI2553TBGP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7752ZHQN/",
"accession": "IGVFFI7752ZHQN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206"
],
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"href": "/configuration-files/IGVFFI7752ZHQN/@@download/IGVFFI7752ZHQN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/88d760d6-75ad-4356-b0e8-cf70e9bff8ba/IGVFFI7752ZHQN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6201YBUU/",
"accession": "IGVFFI6201YBUU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151"
],
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"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0138SEGI/",
"accession": "IGVFFI0138SEGI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7692ITME/",
"accession": "IGVFFI7692ITME",
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],
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"s3_uri": "s3://igvf-files/2024/06/01/3c24a8f3-bd17-4945-b54c-0d9bb32d48ff/IGVFFI7692ITME.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7499BCPY/",
"accession": "IGVFFI7499BCPY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep1_S145"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4194ZWJO/",
"accession": "IGVFFI4194ZWJO",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep2_S200"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5688PYPY/",
"accession": "IGVFFI5688PYPY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep2_S200"
],
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"href": "/configuration-files/IGVFFI5688PYPY/@@download/IGVFFI5688PYPY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b8bdaf17-584c-4bce-a25d-50323f78659c/IGVFFI5688PYPY.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2298KKLO/",
"accession": "IGVFFI2298KKLO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep1_S157"
],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2317UBSQ/",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep1_S145"
],
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"href": "/configuration-files/IGVFFI2317UBSQ/@@download/IGVFFI2317UBSQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/25dbdf84-f72c-4485-bcf4-f783c4244040/IGVFFI2317UBSQ.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7084UIRR/",
"accession": "IGVFFI7084UIRR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151"
],
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"href": "/configuration-files/IGVFFI7084UIRR/@@download/IGVFFI7084UIRR.yaml.gz",
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"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9686UZVW/",
"accession": "IGVFFI9686UZVW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212"
],
"content_type": "seqspec",
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"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI9686UZVW/@@download/IGVFFI9686UZVW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/44cd4480-4f27-4896-815d-6119d3889135/IGVFFI9686UZVW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8267KGLQ/",
"accession": "IGVFDS8267KGLQ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep1_S139",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep1_S145",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep2_S200",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep1_S157",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:22:02.766281+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2548FJWP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2548FJWP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep1_S139",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR1_Rep2_S194",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep1_S145",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR2_Rep2_S200",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep1_S151",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR3_Rep2_S206",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep1_S157",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinE-PCR4_Rep2_S212"
],
"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 E for 80-90% 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": "2024-06-01T02:06:28.028692+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5735424e-47f5-4b5f-a9f1-b2894489f0a8"
}