{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2992RWQM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2992RWQM",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR1_S89",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR2_S95",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR3_S185",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR4_S191"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2992RWQM](/auxiliary-sets/IGVFDS2992RWQM/) has sequence file(s) [IGVFFI5058NVSA](/sequence-files/IGVFFI5058NVSA/), [IGVFFI3817TRUS](/sequence-files/IGVFFI3817TRUS/), [IGVFFI8081SXBE](/sequence-files/IGVFFI8081SXBE/), [IGVFFI0717FWTC](/sequence-files/IGVFFI0717FWTC/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS2992RWQM/"
}
]
},
"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": "2024-05-16T18:01:22.271528+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": [
{
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"accession": "IGVFFI5058NVSA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR1_S89"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:01.724982+00:00",
"file_format": "fastq",
"file_size": 7950075,
"href": "/sequence-files/IGVFFI5058NVSA/@@download/IGVFFI5058NVSA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/326a259b-7e7c-4843-843d-46ffa7ace3fd/IGVFFI5058NVSA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinE-PCR1_S89_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3258XBRG/",
"accession": "IGVFFI3258XBRG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR1_S89"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:26.721606+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI3258XBRG/@@download/IGVFFI3258XBRG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4cbc62e6-963a-4f57-99da-711fded557c4/IGVFFI3258XBRG.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinE-PCR1_S89.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3440BNVL/",
"accession": "IGVFFI3440BNVL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR2_S95"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:41.585857+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI3440BNVL/@@download/IGVFFI3440BNVL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/eb2cab40-9c65-499a-bfc7-bcecd5f14bec/IGVFFI3440BNVL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinE-PCR2_S95.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3308RCCL/",
"accession": "IGVFFI3308RCCL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR4_S191"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:13:10.774659+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI3308RCCL/@@download/IGVFFI3308RCCL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9183b729-5010-41f8-99bc-57c98ea19da7/IGVFFI3308RCCL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinE-PCR4_S191.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3817TRUS/",
"accession": "IGVFFI3817TRUS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR3_S185"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:34.644126+00:00",
"file_format": "fastq",
"file_size": 14750174,
"href": "/sequence-files/IGVFFI3817TRUS/@@download/IGVFFI3817TRUS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/0aa2b7db-0013-4f98-95c0-dcec97b6f78a/IGVFFI3817TRUS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinE-PCR3_S185_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8081SXBE/",
"accession": "IGVFFI8081SXBE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR4_S191"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:51.097232+00:00",
"file_format": "fastq",
"file_size": 16620764,
"href": "/sequence-files/IGVFFI8081SXBE/@@download/IGVFFI8081SXBE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/06176acc-d8e3-4b99-afb2-01016c6f851c/IGVFFI8081SXBE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinE-PCR4_S191_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0717FWTC/",
"accession": "IGVFFI0717FWTC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR2_S95"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-03T15:28:17.678032+00:00",
"file_format": "fastq",
"file_size": 9535085,
"href": "/sequence-files/IGVFFI0717FWTC/@@download/IGVFFI0717FWTC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/fa0d240d-7b87-454f-b2e7-7832df5a083c/IGVFFI0717FWTC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinE-PCR2_S95_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4980WOZN/",
"accession": "IGVFFI4980WOZN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR3_S185"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:56.045536+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4980WOZN/@@download/IGVFFI4980WOZN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a42054ab-1ed8-400b-a049-70414648375d/IGVFFI4980WOZN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinE-PCR3_S185.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4959UVNG/",
"accession": "IGVFDS4959UVNG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR1_S89",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR2_S95",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR3_S185",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR4_S191"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:18:58.098623+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6864OXRH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6864OXRH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR1_S89",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR2_S95",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR3_S185",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinE-PCR4_S191"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"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 KITLG) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T15:28:01.724982+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "6e3676e0-3c3f-4557-97cb-decfafdb280c"
}