{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4662ZYNK/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4662ZYNK",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR1_S40",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR2_S46",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR3_S136",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR4_S142"
],
"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 [IGVFDS4662ZYNK](/auxiliary-sets/IGVFDS4662ZYNK/) has sequence file(s) [IGVFFI8581OGFS](/sequence-files/IGVFFI8581OGFS/), [IGVFFI0805QHNX](/sequence-files/IGVFFI0805QHNX/), [IGVFFI2772MPAA](/sequence-files/IGVFFI2772MPAA/), [IGVFFI3941EFFB](/sequence-files/IGVFFI3941EFFB/) 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/IGVFDS4662ZYNK/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4662ZYNK](/auxiliary-sets/IGVFDS4662ZYNK/) 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/IGVFDS4662ZYNK/"
}
]
},
"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": "2024-05-16T17:42:31.093104+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/IGVFFI8581OGFS/",
"accession": "IGVFFI8581OGFS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR1_S40"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:18:50.195330+00:00",
"file_format": "fastq",
"file_size": 9619742,
"href": "/sequence-files/IGVFFI8581OGFS/@@download/IGVFFI8581OGFS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f44aeb30-aa9e-400a-b5c0-5100a7cc4187/IGVFFI8581OGFS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinD-PCR1_S40_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2277RYFS/",
"accession": "IGVFFI2277RYFS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR1_S40"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:28.687278+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2277RYFS/@@download/IGVFFI2277RYFS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/944b81d4-6bd2-49d6-922b-668ac9aa3302/IGVFFI2277RYFS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinD-PCR1_S40.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0805QHNX/",
"accession": "IGVFFI0805QHNX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR2_S46"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:08.483978+00:00",
"file_format": "fastq",
"file_size": 7815752,
"href": "/sequence-files/IGVFFI0805QHNX/@@download/IGVFFI0805QHNX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a6ea35f6-96c8-4b82-9346-40d5405f75ac/IGVFFI0805QHNX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinD-PCR2_S46_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2772MPAA/",
"accession": "IGVFFI2772MPAA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR3_S136"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:27.378186+00:00",
"file_format": "fastq",
"file_size": 16069913,
"href": "/sequence-files/IGVFFI2772MPAA/@@download/IGVFFI2772MPAA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d1d6d094-a056-4eb0-9efd-50562d419673/IGVFFI2772MPAA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinD-PCR3_S136_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2584CKOF/",
"accession": "IGVFFI2584CKOF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR3_S136"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:56.788772+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI2584CKOF/@@download/IGVFFI2584CKOF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b3718ac7-7461-4adb-8077-e45bdee425de/IGVFFI2584CKOF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinD-PCR3_S136.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2615VRHA/",
"accession": "IGVFFI2615VRHA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR4_S142"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:11.266292+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI2615VRHA/@@download/IGVFFI2615VRHA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b0058e3a-21d1-4b96-b7dd-04b3c90fc25e/IGVFFI2615VRHA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinD-PCR4_S142.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3941EFFB/",
"accession": "IGVFFI3941EFFB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR4_S142"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:45.545927+00:00",
"file_format": "fastq",
"file_size": 11316451,
"href": "/sequence-files/IGVFFI3941EFFB/@@download/IGVFFI3941EFFB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ff0fd6b3-dd27-4106-8509-3abc7d4ac9a8/IGVFFI3941EFFB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinD-PCR4_S142_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4059KFQR/",
"accession": "IGVFFI4059KFQR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR2_S46"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:42.384663+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI4059KFQR/@@download/IGVFFI4059KFQR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cc1d6d53-e165-41ce-a602-7ebc0adcbde8/IGVFFI4059KFQR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinD-PCR2_S46.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0339KYIB/",
"accession": "IGVFDS0339KYIB",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR1_S40",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR2_S46",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR3_S136",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR4_S142"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:16:01.134381+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1961BHPA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1961BHPA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR1_S40",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR2_S46",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR3_S136",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinD-PCR4_S142"
],
"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": "2024-06-01T02:18:50.195330+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c2c33734-8539-43f0-81a5-0c4a3a337b60"
}