{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6385IAUC/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6385IAUC",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR1-Rep1_S134",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR2-Rep1_S140",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR3-Rep1_S188",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR4-Rep1_S194"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9056QVLB](/in-vitro-systems/IGVFSM9056QVLB/) 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/IGVFSM9056QVLB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9056QVLB](/in-vitro-systems/IGVFSM9056QVLB/) 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/IGVFSM9056QVLB/"
},
{
"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 [IGVFDS6385IAUC](/auxiliary-sets/IGVFDS6385IAUC/) has sequence file(s) [IGVFFI8034QLTO](/sequence-files/IGVFFI8034QLTO/), [IGVFFI8323VZPJ](/sequence-files/IGVFFI8323VZPJ/), [IGVFFI6260ZECC](/sequence-files/IGVFFI6260ZECC/), [IGVFFI6399FWUL](/sequence-files/IGVFFI6399FWUL/) 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/IGVFDS6385IAUC/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6385IAUC](/auxiliary-sets/IGVFDS6385IAUC/) 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/IGVFDS6385IAUC/"
}
]
},
"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": "2024-05-14T16:51:07.970433+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",
"files": [
{
"@id": "/sequence-files/IGVFFI8034QLTO/",
"accession": "IGVFFI8034QLTO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR1-Rep1_S134"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:22.793686+00:00",
"file_format": "fastq",
"file_size": 23625367,
"href": "/sequence-files/IGVFFI8034QLTO/@@download/IGVFFI8034QLTO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1f20b8ab-db92-4612-baee-cc4432c18f10/IGVFFI8034QLTO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF1-BinB-PCR1-Rep1_S134_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5421HTOM/",
"accession": "IGVFFI5421HTOM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR1-Rep1_S134"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:43.809332+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5421HTOM/@@download/IGVFFI5421HTOM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5ee029b6-4869-4c69-bd1b-8d7a6e5fb4f9/IGVFFI5421HTOM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinB-PCR1-Rep1_S134.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8323VZPJ/",
"accession": "IGVFFI8323VZPJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR3-Rep1_S188"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:59.351574+00:00",
"file_format": "fastq",
"file_size": 31156876,
"href": "/sequence-files/IGVFFI8323VZPJ/@@download/IGVFFI8323VZPJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9ed0cbaf-e9b5-41b4-81d6-943d0b1b7b4e/IGVFFI8323VZPJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF1-BinB-PCR3-Rep1_S188_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8323GASN/",
"accession": "IGVFFI8323GASN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR4-Rep1_S194"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:25.490692+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8323GASN/@@download/IGVFFI8323GASN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0a0e5acd-69b4-4d16-b3d9-074762da658f/IGVFFI8323GASN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinB-PCR4-Rep1_S194.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6260ZECC/",
"accession": "IGVFFI6260ZECC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR4-Rep1_S194"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:54:17.893115+00:00",
"file_format": "fastq",
"file_size": 29624602,
"href": "/sequence-files/IGVFFI6260ZECC/@@download/IGVFFI6260ZECC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0b40996e-b2d8-4c5a-80aa-b905d4f32c8b/IGVFFI6260ZECC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF1-BinB-PCR4-Rep1_S194_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6399FWUL/",
"accession": "IGVFFI6399FWUL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR2-Rep1_S140"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:40.902661+00:00",
"file_format": "fastq",
"file_size": 16655864,
"href": "/sequence-files/IGVFFI6399FWUL/@@download/IGVFFI6399FWUL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/03e33636-0b54-4e68-a999-495de371d4aa/IGVFFI6399FWUL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin6hrs-FF1-BinB-PCR2-Rep1_S140_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9701XGBH/",
"accession": "IGVFFI9701XGBH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR2-Rep1_S140"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:58.058845+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9701XGBH/@@download/IGVFFI9701XGBH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2b47e4f8-17c1-4c59-a1d4-31e7065be5d1/IGVFFI9701XGBH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinB-PCR2-Rep1_S140.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9865HJQG/",
"accession": "IGVFFI9865HJQG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR3-Rep1_S188"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:44:11.515831+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9865HJQG/@@download/IGVFFI9865HJQG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7890f3b7-1642-4e37-aee1-ec80bf1fb747/IGVFFI9865HJQG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin6hrs-FF1-BinB-PCR3-Rep1_S188.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2171ROQP/",
"accession": "IGVFDS2171ROQP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR1-Rep1_S134",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR2-Rep1_S140",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR3-Rep1_S188",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR4-Rep1_S194"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:12:12.171556+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9056QVLB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9056QVLB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR1-Rep1_S134",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR2-Rep1_S140",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR3-Rep1_S188",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinB-PCR4-Rep1_S194"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"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 FAM3C) 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": "2024-06-01T01:53:22.793686+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3d56e962-c1d1-4857-a51e-fc59778dc783"
}