{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3199FLOT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3199FLOT",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"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 [IGVFDS3199FLOT](/auxiliary-sets/IGVFDS3199FLOT/) has sequence file(s) [IGVFFI9053ATLK](/sequence-files/IGVFFI9053ATLK/), [IGVFFI3274GRZY](/sequence-files/IGVFFI3274GRZY/), [IGVFFI2171OGJO](/sequence-files/IGVFFI2171OGJO/), [IGVFFI9605MXIW](/sequence-files/IGVFFI9605MXIW/) 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/IGVFDS3199FLOT/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3199FLOT](/auxiliary-sets/IGVFDS3199FLOT/) 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/IGVFDS3199FLOT/"
}
]
},
"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": "2024-05-16T17:41:00.833329+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/IGVFFI9053ATLK/",
"accession": "IGVFFI9053ATLK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:10:11.339608+00:00",
"file_format": "fastq",
"file_size": 10662322,
"href": "/sequence-files/IGVFFI9053ATLK/@@download/IGVFFI9053ATLK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2ffb14a1-4976-4f07-9d8b-2b1ac7da8848/IGVFFI9053ATLK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR1_S1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8642JEKZ/",
"accession": "IGVFFI8642JEKZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:27.129924+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI8642JEKZ/@@download/IGVFFI8642JEKZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b49bc8c0-8ece-45ad-866c-a87b53780364/IGVFFI8642JEKZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR1_S1.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3274GRZY/",
"accession": "IGVFFI3274GRZY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:11:10.226683+00:00",
"file_format": "fastq",
"file_size": 20053603,
"href": "/sequence-files/IGVFFI3274GRZY/@@download/IGVFFI3274GRZY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/90ae2cb4-44ec-473d-8e7f-d041642ab65c/IGVFFI3274GRZY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR4_S103_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2171OGJO/",
"accession": "IGVFFI2171OGJO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:10:30.356025+00:00",
"file_format": "fastq",
"file_size": 8424943,
"href": "/sequence-files/IGVFFI2171OGJO/@@download/IGVFFI2171OGJO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8c93e09f-6315-48be-a9a5-760c1ee09024/IGVFFI2171OGJO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR2_S7_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8677QAFW/",
"accession": "IGVFFI8677QAFW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:08.193076+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8677QAFW/@@download/IGVFFI8677QAFW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f559802a-e29a-4055-8dd7-57e4bd29b6ed/IGVFFI8677QAFW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR3_S97.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4323OUFB/",
"accession": "IGVFFI4323OUFB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:21.523457+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI4323OUFB/@@download/IGVFFI4323OUFB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/bdf95efb-ed69-4006-979c-4866ade46c1f/IGVFFI4323OUFB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR4_S103.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9605MXIW/",
"accession": "IGVFFI9605MXIW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:10:52.072437+00:00",
"file_format": "fastq",
"file_size": 36290095,
"href": "/sequence-files/IGVFFI9605MXIW/@@download/IGVFFI9605MXIW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/03ddcdcd-6ff3-4326-953b-d55ac9f7d0dc/IGVFFI9605MXIW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR3_S97_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8363ADQK/",
"accession": "IGVFFI8363ADQK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:54.683371+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI8363ADQK/@@download/IGVFFI8363ADQK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0ea6d0f8-a3c1-40c2-b6c2-10325701ac3f/IGVFFI8363ADQK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR2_S7.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9168ZKDC/",
"accession": "IGVFDS9168ZKDC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:13:31.315752+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8111MLZW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8111MLZW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"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 A for 0-10% 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": "2024-06-01T02:10:11.339608+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "17e83993-00ef-41b6-af08-0d1828865ffa"
}