{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1635IQIT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1635IQIT",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"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 [IGVFDS1635IQIT](/auxiliary-sets/IGVFDS1635IQIT/) has sequence file(s) [IGVFFI0357RECW](/sequence-files/IGVFFI0357RECW/), [IGVFFI0079YAMM](/sequence-files/IGVFFI0079YAMM/), [IGVFFI7682PLQL](/sequence-files/IGVFFI7682PLQL/), [IGVFFI2660UTOF](/sequence-files/IGVFFI2660UTOF/) 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/IGVFDS1635IQIT/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1635IQIT](/auxiliary-sets/IGVFDS1635IQIT/) 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/IGVFDS1635IQIT/"
}
]
},
"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": "2024-05-16T17:41:02.269582+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/IGVFFI0357RECW/",
"accession": "IGVFFI0357RECW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:10:14.444737+00:00",
"file_format": "fastq",
"file_size": 17777080,
"href": "/sequence-files/IGVFFI0357RECW/@@download/IGVFFI0357RECW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d6ba4e2b-9d9d-46d5-abd2-fbf5ae98274c/IGVFFI0357RECW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinB-PCR1_S2_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6958FQNG/",
"accession": "IGVFFI6958FQNG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:42.644512+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI6958FQNG/@@download/IGVFFI6958FQNG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9ffcc9c7-bcb3-429a-96b5-1c0b91fc3d22/IGVFFI6958FQNG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR1_S2.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3962TRBT/",
"accession": "IGVFFI3962TRBT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:56.882382+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI3962TRBT/@@download/IGVFFI3962TRBT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4b2aa2a9-fc18-40cf-8d5d-5abf28eccf8f/IGVFFI3962TRBT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR2_S8.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8059ZOIT/",
"accession": "IGVFFI8059ZOIT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:23.697671+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8059ZOIT/@@download/IGVFFI8059ZOIT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/e99a5bd6-3a30-4e37-b249-9134d0cedd17/IGVFFI8059ZOIT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR4_S104.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0079YAMM/",
"accession": "IGVFFI0079YAMM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:10:55.160854+00:00",
"file_format": "fastq",
"file_size": 40391210,
"href": "/sequence-files/IGVFFI0079YAMM/@@download/IGVFFI0079YAMM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c37dea70-4c22-471e-8ef0-97af0e2f5a4e/IGVFFI0079YAMM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinB-PCR3_S98_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7682PLQL/",
"accession": "IGVFFI7682PLQL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:11:13.396167+00:00",
"file_format": "fastq",
"file_size": 23961767,
"href": "/sequence-files/IGVFFI7682PLQL/@@download/IGVFFI7682PLQL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/331fdc20-281c-4047-9495-aae48f0a4a43/IGVFFI7682PLQL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinB-PCR4_S104_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2660UTOF/",
"accession": "IGVFFI2660UTOF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:10:33.277352+00:00",
"file_format": "fastq",
"file_size": 12033624,
"href": "/sequence-files/IGVFFI2660UTOF/@@download/IGVFFI2660UTOF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9e67465c-0499-4e06-8669-943c21a7644b/IGVFFI2660UTOF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinB-PCR2_S8_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6721VKWR/",
"accession": "IGVFFI6721VKWR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:10.471658+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI6721VKWR/@@download/IGVFFI6721VKWR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/712800c8-4045-4c16-949c-b8ae61f947cf/IGVFFI6721VKWR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinB-PCR3_S98.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1679JOIX/",
"accession": "IGVFDS1679JOIX",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:13:38.706593+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4469TBGW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4469TBGW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR1_S2",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR2_S8",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR3_S98",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinB-PCR4_S104"
],
"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 B for 10-20% 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": "2024-06-01T02:10:14.444737+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d40ee258-469a-4fd8-82ae-05563be7388b"
}