{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2086YDNO/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2086YDNO",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6859FEHH](/in-vitro-systems/IGVFSM6859FEHH/) 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/IGVFSM6859FEHH/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6859FEHH](/in-vitro-systems/IGVFSM6859FEHH/) 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/IGVFSM6859FEHH/"
},
{
"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 [IGVFDS2086YDNO](/auxiliary-sets/IGVFDS2086YDNO/) has sequence file(s) [IGVFFI6411ZRDE](/sequence-files/IGVFFI6411ZRDE/), [IGVFFI9315VFMT](/sequence-files/IGVFFI9315VFMT/), [IGVFFI2101KHOH](/sequence-files/IGVFFI2101KHOH/), [IGVFFI8335UTTJ](/sequence-files/IGVFFI8335UTTJ/) 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/IGVFDS2086YDNO/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2086YDNO](/auxiliary-sets/IGVFDS2086YDNO/) 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/IGVFDS2086YDNO/"
}
]
},
"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": "2024-05-16T17:58:54.936910+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/IGVFFI6411ZRDE/",
"accession": "IGVFFI6411ZRDE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:56.748397+00:00",
"file_format": "fastq",
"file_size": 11164702,
"href": "/sequence-files/IGVFFI6411ZRDE/@@download/IGVFFI6411ZRDE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/058fb837-83b6-4c6f-aa8b-59241add2d18/IGVFFI6411ZRDE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinA-PCR1_S49_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0901ITUC/",
"accession": "IGVFFI0901ITUC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:18.336327+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI0901ITUC/@@download/IGVFFI0901ITUC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/05c50283-db8e-4fa1-b123-1499d2fc2dbb/IGVFFI0901ITUC.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR1_S49.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9315VFMT/",
"accession": "IGVFFI9315VFMT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:37.436735+00:00",
"file_format": "fastq",
"file_size": 25312994,
"href": "/sequence-files/IGVFFI9315VFMT/@@download/IGVFFI9315VFMT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/553b5cd2-e3d5-4615-a5e6-c3160b9e2113/IGVFFI9315VFMT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinA-PCR3_S145_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2101KHOH/",
"accession": "IGVFFI2101KHOH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:16.661412+00:00",
"file_format": "fastq",
"file_size": 7121098,
"href": "/sequence-files/IGVFFI2101KHOH/@@download/IGVFFI2101KHOH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bcd1b250-72c0-4803-a923-974b92d2ce81/IGVFFI2101KHOH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinA-PCR2_S55_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8335UTTJ/",
"accession": "IGVFFI8335UTTJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:20:55.444582+00:00",
"file_format": "fastq",
"file_size": 19453121,
"href": "/sequence-files/IGVFFI8335UTTJ/@@download/IGVFFI8335UTTJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/28652d54-f5e3-4b2d-bdb1-01593b2276e9/IGVFFI8335UTTJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF1-BinA-PCR4_S151_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2519BAOP/",
"accession": "IGVFFI2519BAOP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:10:03.708778+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI2519BAOP/@@download/IGVFFI2519BAOP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f2948797-08ea-4bda-86d7-ce0265e556a4/IGVFFI2519BAOP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR4_S151.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1495XMKJ/",
"accession": "IGVFFI1495XMKJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:33.858069+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1495XMKJ/@@download/IGVFFI1495XMKJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b83b3244-af65-4059-bf1f-1270ea8d3ba4/IGVFFI1495XMKJ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR2_S55.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1838QYEH/",
"accession": "IGVFFI1838QYEH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:48.811023+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI1838QYEH/@@download/IGVFFI1838QYEH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f6a9caec-7bb3-441a-a27d-706009db62d6/IGVFFI1838QYEH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF1-BinA-PCR3_S145.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1505VYUV/",
"accession": "IGVFDS1505VYUV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:16:20.905833+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6859FEHH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6859FEHH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR1_S49",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR2_S55",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR3_S145",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF1-BinA-PCR4_S151"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7846UISG/"
],
"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 A for 0-10% expression of KITLG) 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": "2024-06-01T02:19:56.748397+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "2305767d-d7ea-42c8-a7cd-b9c734509091"
}