{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5649QCUR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5649QCUR",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR1_S85",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR2_S91",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR3_S181",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR4_S187"
],
"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/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8950GODK](/in-vitro-systems/IGVFSM8950GODK/) 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/IGVFSM8950GODK/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8950GODK](/in-vitro-systems/IGVFSM8950GODK/) 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/IGVFSM8950GODK/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5649QCUR](/auxiliary-sets/IGVFDS5649QCUR/) has sequence file(s) [IGVFFI9119ACAF](/sequence-files/IGVFFI9119ACAF/), [IGVFFI6782WVEI](/sequence-files/IGVFFI6782WVEI/), [IGVFFI6804OFIF](/sequence-files/IGVFFI6804OFIF/), [IGVFFI0631OAFL](/sequence-files/IGVFFI0631OAFL/) 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/IGVFDS5649QCUR/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5649QCUR](/auxiliary-sets/IGVFDS5649QCUR/) 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/IGVFDS5649QCUR/"
}
]
},
"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": "2024-05-16T18:01:18.812370+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/IGVFFI9119ACAF/",
"accession": "IGVFFI9119ACAF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR1_S85"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:27:51.283092+00:00",
"file_format": "fastq",
"file_size": 8176381,
"href": "/sequence-files/IGVFFI9119ACAF/@@download/IGVFFI9119ACAF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/4a71eaa2-5c22-451e-829b-bfb71815044f/IGVFFI9119ACAF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinA-PCR1_S85_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4047XDKV/",
"accession": "IGVFFI4047XDKV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR1_S85"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:17.205570+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI4047XDKV/@@download/IGVFFI4047XDKV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/49608d4c-262f-41ed-9237-a8b6d852d704/IGVFFI4047XDKV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinA-PCR1_S85.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5704IPMB/",
"accession": "IGVFFI5704IPMB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR3_S181"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:46.425631+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI5704IPMB/@@download/IGVFFI5704IPMB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a230119a-4d6f-43c9-b31d-b8e711eb4443/IGVFFI5704IPMB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinA-PCR3_S181.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6782WVEI/",
"accession": "IGVFFI6782WVEI",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR2_S91"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:07.217569+00:00",
"file_format": "fastq",
"file_size": 5310230,
"href": "/sequence-files/IGVFFI6782WVEI/@@download/IGVFFI6782WVEI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/fbf48fa5-de64-4125-b27f-7dc91e9cc8d2/IGVFFI6782WVEI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinA-PCR2_S91_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6804OFIF/",
"accession": "IGVFFI6804OFIF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR4_S187"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:39.917328+00:00",
"file_format": "fastq",
"file_size": 8378830,
"href": "/sequence-files/IGVFFI6804OFIF/@@download/IGVFFI6804OFIF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/8dda281a-50e8-4b57-8fc4-1bebdc9501be/IGVFFI6804OFIF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinA-PCR4_S187_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1517OVUR/",
"accession": "IGVFFI1517OVUR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR4_S187"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:13:01.148733+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI1517OVUR/@@download/IGVFFI1517OVUR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/946d3bad-87b9-4347-9832-ea3ae4453dee/IGVFFI1517OVUR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinA-PCR4_S187.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0631OAFL/",
"accession": "IGVFFI0631OAFL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR3_S181"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T15:28:23.062874+00:00",
"file_format": "fastq",
"file_size": 21503611,
"href": "/sequence-files/IGVFFI0631OAFL/@@download/IGVFFI0631OAFL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/d2429a14-319e-488d-ac38-f266e6ce1f1b/IGVFFI0631OAFL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin6hrs-FF4-BinA-PCR3_S181_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4548IETV/",
"accession": "IGVFFI4548IETV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR2_S91"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:12:31.474913+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI4548IETV/@@download/IGVFFI4548IETV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d9e40860-bd24-4d3b-ad24-65ab49665f1d/IGVFFI4548IETV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin6hrs-FF4-BinA-PCR2_S91.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4850YYRL/",
"accession": "IGVFDS4850YYRL",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR1_S85",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR2_S91",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR3_S181",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR4_S187"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:18:30.724845+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8950GODK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8950GODK",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR1_S85",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR2_S91",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR3_S181",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin6hrs-FF4-BinA-PCR4_S187"
],
"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": "2024-06-03T15:27:51.283092+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b6626258-4405-414d-9aa5-9e44fa710ce2"
}