{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5688OXJC/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5688OXJC",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"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 [IGVFDS5688OXJC](/auxiliary-sets/IGVFDS5688OXJC/) has sequence file(s) [IGVFFI5281RKUY](/sequence-files/IGVFFI5281RKUY/), [IGVFFI7621INKU](/sequence-files/IGVFFI7621INKU/), [IGVFFI2546PANA](/sequence-files/IGVFFI2546PANA/), [IGVFFI7661OGMF](/sequence-files/IGVFFI7661OGMF/) 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/IGVFDS5688OXJC/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5688OXJC](/auxiliary-sets/IGVFDS5688OXJC/) 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/IGVFDS5688OXJC/"
}
]
},
"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": "2024-05-16T17:41:30.572418+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/IGVFFI5281RKUY/",
"accession": "IGVFFI5281RKUY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:35.717978+00:00",
"file_format": "fastq",
"file_size": 6946133,
"href": "/sequence-files/IGVFFI5281RKUY/@@download/IGVFFI5281RKUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fc535ec7-9112-4d77-bc2e-0338806cabea/IGVFFI5281RKUY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinC-PCR1_S15_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5011CJLO/",
"accession": "IGVFFI5011CJLO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:39.581219+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI5011CJLO/@@download/IGVFFI5011CJLO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d56f94f5-4493-463c-ac12-7fc1618f92c2/IGVFFI5011CJLO.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinC-PCR1_S15.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7621INKU/",
"accession": "IGVFFI7621INKU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:16:55.027578+00:00",
"file_format": "fastq",
"file_size": 19998267,
"href": "/sequence-files/IGVFFI7621INKU/@@download/IGVFFI7621INKU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f7118058-6f0e-4230-8399-cf60bbb201b5/IGVFFI7621INKU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinC-PCR3_S111_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2546PANA/",
"accession": "IGVFFI2546PANA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:53.237438+00:00",
"file_format": "fastq",
"file_size": 11153667,
"href": "/sequence-files/IGVFFI2546PANA/@@download/IGVFFI2546PANA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/929e418e-cc00-48f2-aba6-628eacc7fc16/IGVFFI2546PANA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinC-PCR2_S21_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7661OGMF/",
"accession": "IGVFFI7661OGMF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:13.386802+00:00",
"file_format": "fastq",
"file_size": 22508303,
"href": "/sequence-files/IGVFFI7661OGMF/@@download/IGVFFI7661OGMF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/386ea676-72f7-44e5-9167-891f95b10ee2/IGVFFI7661OGMF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinC-PCR4_S117_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0460DWZH/",
"accession": "IGVFFI0460DWZH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:19.967412+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0460DWZH/@@download/IGVFFI0460DWZH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/566285eb-cbf9-4db0-9982-b045981fbf0c/IGVFFI0460DWZH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinC-PCR4_S117.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0383OYTL/",
"accession": "IGVFFI0383OYTL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:53.295311+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI0383OYTL/@@download/IGVFFI0383OYTL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/14d04f53-789f-44ce-a07c-81fcc9c79cd4/IGVFFI0383OYTL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinC-PCR2_S21.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5915HQEK/",
"accession": "IGVFFI5915HQEK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:06.827765+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI5915HQEK/@@download/IGVFFI5915HQEK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f1997c14-a1c0-405b-85da-815d481005fe/IGVFFI5915HQEK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinC-PCR3_S111.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9308CBBI/",
"accession": "IGVFDS9308CBBI",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:14:27.429138+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7071BULA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7071BULA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117"
],
"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 C for 35-45% 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": "2024-06-01T02:14:35.717978+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "fbb50ae3-0460-48a0-9414-7ff400219b33"
}