{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8719WWWS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8719WWWS",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"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/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8719WWWS](/auxiliary-sets/IGVFDS8719WWWS/) has sequence file(s) [IGVFFI1457EKWS](/sequence-files/IGVFFI1457EKWS/), [IGVFFI6514JTIC](/sequence-files/IGVFFI6514JTIC/), [IGVFFI4376KAKY](/sequence-files/IGVFFI4376KAKY/), [IGVFFI4369YDEU](/sequence-files/IGVFFI4369YDEU/) 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/IGVFDS8719WWWS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8719WWWS](/auxiliary-sets/IGVFDS8719WWWS/) 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/IGVFDS8719WWWS/"
}
]
},
"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": "2024-05-16T17:41:59.769246+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/IGVFFI1457EKWS/",
"accession": "IGVFFI1457EKWS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:33.774408+00:00",
"file_format": "fastq",
"file_size": 9690717,
"href": "/sequence-files/IGVFFI1457EKWS/@@download/IGVFFI1457EKWS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0e9b4aa7-de8e-495d-b4ac-7457d0263f91/IGVFFI1457EKWS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinD-PCR1_S28_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1149KOYD/",
"accession": "IGVFFI1149KOYD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:35.760798+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1149KOYD/@@download/IGVFFI1149KOYD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5efd1b99-5540-4a78-9c05-4fd02b7ae686/IGVFFI1149KOYD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR1_S28.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6514JTIC/",
"accession": "IGVFFI6514JTIC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:18:09.739332+00:00",
"file_format": "fastq",
"file_size": 14976861,
"href": "/sequence-files/IGVFFI6514JTIC/@@download/IGVFFI6514JTIC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1e3ad7b9-fb63-41a1-a4cd-cdd3cac19a9a/IGVFFI6514JTIC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinD-PCR3_S124_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5189ZWRI/",
"accession": "IGVFFI5189ZWRI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:15.623998+00:00",
"file_format": "yaml",
"file_size": 905,
"href": "/configuration-files/IGVFFI5189ZWRI/@@download/IGVFFI5189ZWRI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b8c5f31f-2cde-4c8e-8afe-0b59ca558b9b/IGVFFI5189ZWRI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR4_S130.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7135SUWD/",
"accession": "IGVFFI7135SUWD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:49.107063+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI7135SUWD/@@download/IGVFFI7135SUWD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7b91610b-f973-4802-8c66-6dcf41ff21ac/IGVFFI7135SUWD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR2_S34.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4376KAKY/",
"accession": "IGVFFI4376KAKY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:51.855556+00:00",
"file_format": "fastq",
"file_size": 10933667,
"href": "/sequence-files/IGVFFI4376KAKY/@@download/IGVFFI4376KAKY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/09edb302-5744-4d76-99bc-fc8459a75105/IGVFFI4376KAKY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinD-PCR2_S34_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4369YDEU/",
"accession": "IGVFFI4369YDEU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:18:27.785290+00:00",
"file_format": "fastq",
"file_size": 20531648,
"href": "/sequence-files/IGVFFI4369YDEU/@@download/IGVFFI4369YDEU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1a7b76b3-afd6-40ed-aa66-fce0d3509606/IGVFFI4369YDEU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF3-BinD-PCR4_S130_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1137LHCT/",
"accession": "IGVFFI1137LHCT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:02.351965+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI1137LHCT/@@download/IGVFFI1137LHCT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0aae9ad4-6a8b-4540-a350-d8d1ab9f87bd/IGVFFI1137LHCT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF3-BinD-PCR3_S124.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6007VHUG/",
"accession": "IGVFDS6007VHUG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:15:16.857439+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3068ZYXS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3068ZYXS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR1_S28",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR2_S34",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR3_S124",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF3-BinD-PCR4_S130"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"modifications": [
"/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 D for 55-65% expression of KITLG) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:17:33.774408+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "2e297e60-bd99-4078-af3f-5475a668965b"
}