{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5076XXNM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5076XXNM",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR1_S39",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR2_S45",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR3_S135",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR4_S141"
],
"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 [IGVFDS5076XXNM](/auxiliary-sets/IGVFDS5076XXNM/) has sequence file(s) [IGVFFI8486BPIR](/sequence-files/IGVFFI8486BPIR/), [IGVFFI9114UFQH](/sequence-files/IGVFFI9114UFQH/), [IGVFFI1234CFBG](/sequence-files/IGVFFI1234CFBG/), [IGVFFI6708IHTH](/sequence-files/IGVFFI6708IHTH/) 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/IGVFDS5076XXNM/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5076XXNM](/auxiliary-sets/IGVFDS5076XXNM/) 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/IGVFDS5076XXNM/"
}
]
},
"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": "2024-05-16T17:42:29.821519+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/IGVFFI8486BPIR/",
"accession": "IGVFFI8486BPIR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR1_S39"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:18:47.030734+00:00",
"file_format": "fastq",
"file_size": 12885963,
"href": "/sequence-files/IGVFFI8486BPIR/@@download/IGVFFI8486BPIR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/04d743ef-15ea-43bb-a393-f106a50219d8/IGVFFI8486BPIR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinC-PCR1_S39_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0311DANT/",
"accession": "IGVFFI0311DANT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR1_S39"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:26.564717+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI0311DANT/@@download/IGVFFI0311DANT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d7e288b3-c8c4-4593-b3a1-b9a4daeaa6c0/IGVFFI0311DANT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinC-PCR1_S39.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9114UFQH/",
"accession": "IGVFFI9114UFQH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR3_S135"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:23.923827+00:00",
"file_format": "fastq",
"file_size": 18100498,
"href": "/sequence-files/IGVFFI9114UFQH/@@download/IGVFFI9114UFQH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/11641827-42b9-4084-9577-0c819d49bd35/IGVFFI9114UFQH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinC-PCR3_S135_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1234CFBG/",
"accession": "IGVFFI1234CFBG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR4_S141"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:42.531468+00:00",
"file_format": "fastq",
"file_size": 21550469,
"href": "/sequence-files/IGVFFI1234CFBG/@@download/IGVFFI1234CFBG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6b6ad5bd-3eb7-412e-96a7-20f47b59ea3d/IGVFFI1234CFBG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinC-PCR4_S141_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8934DFKM/",
"accession": "IGVFFI8934DFKM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR3_S135"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:54.452383+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI8934DFKM/@@download/IGVFFI8934DFKM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/df3478de-c44f-48b0-ad60-3e7c91defc15/IGVFFI8934DFKM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinC-PCR3_S135.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1343ZHUK/",
"accession": "IGVFFI1343ZHUK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR4_S141"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:08.923996+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI1343ZHUK/@@download/IGVFFI1343ZHUK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3df813f7-3035-4cf9-bc6e-792b55dc60ca/IGVFFI1343ZHUK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinC-PCR4_S141.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6708IHTH/",
"accession": "IGVFFI6708IHTH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR2_S45"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:04.870058+00:00",
"file_format": "fastq",
"file_size": 10935672,
"href": "/sequence-files/IGVFFI6708IHTH/@@download/IGVFFI6708IHTH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/424a1339-c1c7-4c2c-816d-7f810d5753db/IGVFFI6708IHTH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinC-PCR2_S45_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0256KDQX/",
"accession": "IGVFFI0256KDQX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR2_S45"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:39.972978+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI0256KDQX/@@download/IGVFFI0256KDQX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c7cf390a-b635-456d-bb2b-d8bc0e4af12d/IGVFFI0256KDQX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinC-PCR2_S45.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0488GVJK/",
"accession": "IGVFDS0488GVJK",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR1_S39",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR2_S45",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR3_S135",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR4_S141"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:15:53.819142+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2659OCKX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2659OCKX",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR1_S39",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR2_S45",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR3_S135",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinC-PCR4_S141"
],
"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 C for 35-45% 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": "2024-06-01T02:18:47.030734+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "59bee6e4-1143-4437-9472-1ab8c724da1a"
}