{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2251KSGP/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2251KSGP",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109"
],
"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 [IGVFDS2251KSGP](/auxiliary-sets/IGVFDS2251KSGP/) has sequence file(s) [IGVFFI3592XQZL](/sequence-files/IGVFFI3592XQZL/), [IGVFFI6736AYSD](/sequence-files/IGVFFI6736AYSD/), [IGVFFI5346NUQZ](/sequence-files/IGVFFI5346NUQZ/), [IGVFFI8656RWXA](/sequence-files/IGVFFI8656RWXA/) 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/IGVFDS2251KSGP/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2251KSGP](/auxiliary-sets/IGVFDS2251KSGP/) 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/IGVFDS2251KSGP/"
}
]
},
"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": "2024-05-16T17:41:28.086815+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/IGVFFI3592XQZL/",
"accession": "IGVFFI3592XQZL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:29.539667+00:00",
"file_format": "fastq",
"file_size": 13456146,
"href": "/sequence-files/IGVFFI3592XQZL/@@download/IGVFFI3592XQZL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/422b3fa6-d82b-46b3-86bf-705a9ccca1a4/IGVFFI3592XQZL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinA-PCR1_S13_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6317BSBL/",
"accession": "IGVFFI6317BSBL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:35.312395+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI6317BSBL/@@download/IGVFFI6317BSBL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/09d17721-93d8-4229-987a-df3490d496dd/IGVFFI6317BSBL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinA-PCR1_S13.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6736AYSD/",
"accession": "IGVFFI6736AYSD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:14:47.344896+00:00",
"file_format": "fastq",
"file_size": 10477762,
"href": "/sequence-files/IGVFFI6736AYSD/@@download/IGVFFI6736AYSD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6f55cbd7-8038-4b9e-9eca-85240a2c7fe5/IGVFFI6736AYSD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinA-PCR2_S19_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5346NUQZ/",
"accession": "IGVFFI5346NUQZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:17:07.282030+00:00",
"file_format": "fastq",
"file_size": 22023359,
"href": "/sequence-files/IGVFFI5346NUQZ/@@download/IGVFFI5346NUQZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/af6314c3-7a6d-4b1d-88ab-5285ac97d6c8/IGVFFI5346NUQZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinA-PCR4_S115_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8656RWXA/",
"accession": "IGVFFI8656RWXA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:16:48.948175+00:00",
"file_format": "fastq",
"file_size": 39042526,
"href": "/sequence-files/IGVFFI8656RWXA/@@download/IGVFFI8656RWXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4a6b87d9-f754-4ec6-9dd7-6e3b3027b4de/IGVFFI8656RWXA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF2-BinA-PCR3_S109_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6590TUUT/",
"accession": "IGVFFI6590TUUT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:48.568457+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI6590TUUT/@@download/IGVFFI6590TUUT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/99a1c76a-8aee-4ed5-b4ae-34d7b3b37b6e/IGVFFI6590TUUT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinA-PCR2_S19.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3114INON/",
"accession": "IGVFFI3114INON",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:15.539236+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI3114INON/@@download/IGVFFI3114INON.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/16ba4143-51dd-49f3-86d4-a9c9318a8d7f/IGVFFI3114INON.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinA-PCR4_S115.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0792VIBF/",
"accession": "IGVFFI0792VIBF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:07:02.254578+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0792VIBF/@@download/IGVFFI0792VIBF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fa25a008-32d0-4577-9660-dbcf079cc3b9/IGVFFI0792VIBF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF2-BinA-PCR3_S109.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4649YECB/",
"accession": "IGVFDS4649YECB",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S109"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"notes": "The original alias jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S109 was changed to jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109",
"release_timestamp": "2024-07-10T20:14:13.417961+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8346JZPG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8346JZPG",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR1_S13",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR2_S19",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR4_S115",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF2-BinA-PCR3_S109"
],
"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": "2024-06-01T02:14:29.539667+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "298548c4-2698-47f2-af3a-1cda8d35f232"
}