{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6495PTGH/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6495PTGH",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133",
"jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"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 [IGVFDS6495PTGH](/auxiliary-sets/IGVFDS6495PTGH/) has sequence file(s) [IGVFFI7682XDAF](/sequence-files/IGVFFI7682XDAF/), [IGVFFI3780QMCR](/sequence-files/IGVFFI3780QMCR/), [IGVFFI8017EEHN](/sequence-files/IGVFFI8017EEHN/), [IGVFFI1299YDLA](/sequence-files/IGVFFI1299YDLA/) 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/IGVFDS6495PTGH/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6495PTGH](/auxiliary-sets/IGVFDS6495PTGH/) 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/IGVFDS6495PTGH/"
}
]
},
"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": "2024-05-16T17:42:27.275747+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/IGVFFI7682XDAF/",
"accession": "IGVFFI7682XDAF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:18:40.906870+00:00",
"file_format": "fastq",
"file_size": 11269013,
"href": "/sequence-files/IGVFFI7682XDAF/@@download/IGVFFI7682XDAF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/27d19971-49e6-4137-93d3-77a7d7e8b376/IGVFFI7682XDAF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinA-PCR1_S37_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9566VEHX/",
"accession": "IGVFFI9566VEHX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:22.127329+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI9566VEHX/@@download/IGVFFI9566VEHX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ef9acef7-a87b-4286-bede-afb97cbedd03/IGVFFI9566VEHX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinA-PCR1_S37.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3780QMCR/",
"accession": "IGVFFI3780QMCR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:18.070838+00:00",
"file_format": "fastq",
"file_size": 23790861,
"href": "/sequence-files/IGVFFI3780QMCR/@@download/IGVFFI3780QMCR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b0425bfe-1c32-4b92-aaab-a28e2d29d63b/IGVFFI3780QMCR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinA-PCR3_S133_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8017EEHN/",
"accession": "IGVFFI8017EEHN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:19:36.424657+00:00",
"file_format": "fastq",
"file_size": 19687583,
"href": "/sequence-files/IGVFFI8017EEHN/@@download/IGVFFI8017EEHN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/45c8401c-2bf5-4016-9d88-f13e531bc10c/IGVFFI8017EEHN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinA-PCR4_S139_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9850DZDZ/",
"accession": "IGVFFI9850DZDZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:35.351205+00:00",
"file_format": "yaml",
"file_size": 903,
"href": "/configuration-files/IGVFFI9850DZDZ/@@download/IGVFFI9850DZDZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cd0cab8e-0cc9-47c0-bf02-85b08a4ece58/IGVFFI9850DZDZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinA-PCR2_S43.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6476ZXDT/",
"accession": "IGVFFI6476ZXDT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:08:49.527632+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI6476ZXDT/@@download/IGVFFI6476ZXDT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d5c134bf-1eab-47ce-827e-236e2698a3e1/IGVFFI6476ZXDT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinA-PCR3_S133.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1299YDLA/",
"accession": "IGVFFI1299YDLA",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:18:59.016448+00:00",
"file_format": "fastq",
"file_size": 11266830,
"href": "/sequence-files/IGVFFI1299YDLA/@@download/IGVFFI1299YDLA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/1ca406a2-e58d-489b-bd81-7f2fb3996757/IGVFFI1299YDLA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF4-BinA-PCR2_S43_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9458GGZZ/",
"accession": "IGVFFI9458GGZZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:09:03.898587+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI9458GGZZ/@@download/IGVFFI9458GGZZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/758b4238-9ba5-46b3-9f78-230a5937c247/IGVFFI9458GGZZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF4-BinA-PCR4_S139.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1681VDMR/",
"accession": "IGVFDS1681VDMR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:15:38.605168+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1476GCQU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1476GCQU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR1_S37",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR2_S43",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR3_S133",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF4-BinA-PCR4_S139"
],
"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": "2024-06-01T02:18:40.906870+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d5c52298-61c3-4022-9836-b94aff8044a3"
}