{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6870QBVM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6870QBVM",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"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 [IGVFDS6870QBVM](/auxiliary-sets/IGVFDS6870QBVM/) has sequence file(s) [IGVFFI3952UPLD](/sequence-files/IGVFFI3952UPLD/), [IGVFFI5250HUCB](/sequence-files/IGVFFI5250HUCB/), [IGVFFI3227NNAQ](/sequence-files/IGVFFI3227NNAQ/), [IGVFFI8622TDNM](/sequence-files/IGVFFI8622TDNM/) 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/IGVFDS6870QBVM/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6870QBVM](/auxiliary-sets/IGVFDS6870QBVM/) 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/IGVFDS6870QBVM/"
}
]
},
"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": "2024-05-14T20:31:20.203361+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/IGVFFI3952UPLD/",
"accession": "IGVFFI3952UPLD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:45:53.847312+00:00",
"file_format": "fastq",
"file_size": 10849000,
"href": "/sequence-files/IGVFFI3952UPLD/@@download/IGVFFI3952UPLD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dbad0f22-1fd8-4b58-b661-6ffecce5e1de/IGVFFI3952UPLD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7304ZIDV/",
"accession": "IGVFFI7304ZIDV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:22.733909+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI7304ZIDV/@@download/IGVFFI7304ZIDV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/45dafe10-cc14-47ba-be08-9df070501866/IGVFFI7304ZIDV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5250HUCB/",
"accession": "IGVFFI5250HUCB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:15.727706+00:00",
"file_format": "fastq",
"file_size": 15820281,
"href": "/sequence-files/IGVFFI5250HUCB/@@download/IGVFFI5250HUCB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2f41b100-9878-4c19-9a4d-eec07d690cb1/IGVFFI5250HUCB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3227NNAQ/",
"accession": "IGVFFI3227NNAQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:34.986333+00:00",
"file_format": "fastq",
"file_size": 20511350,
"href": "/sequence-files/IGVFFI3227NNAQ/@@download/IGVFFI3227NNAQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8037516d-443c-4325-a655-3ce9d33cbfee/IGVFFI3227NNAQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8622TDNM/",
"accession": "IGVFFI8622TDNM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:46:52.829493+00:00",
"file_format": "fastq",
"file_size": 18707865,
"href": "/sequence-files/IGVFFI8622TDNM/@@download/IGVFFI8622TDNM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f7e7249d-8f13-4cd1-80b6-6a173dc1cdf8/IGVFFI8622TDNM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9956XLRB/",
"accession": "IGVFFI9956XLRB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:38:38.329827+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI9956XLRB/@@download/IGVFFI9956XLRB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a49fe185-b57b-479b-ac0e-20c207debad4/IGVFFI9956XLRB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2564WQBV/",
"accession": "IGVFFI2564WQBV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:16.887824+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI2564WQBV/@@download/IGVFFI2564WQBV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ac60fe2b-9bef-492f-999f-ceeb4e6e4828/IGVFFI2564WQBV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2975BGQX/",
"accession": "IGVFFI2975BGQX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:39:32.374733+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2975BGQX/@@download/IGVFFI2975BGQX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ee30c74a-1e96-4a58-a8ed-4c66c2be8ca8/IGVFFI2975BGQX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6103MEVT/",
"accession": "IGVFDS6103MEVT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:24:40.367999+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8438GPDC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8438GPDC",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR1-Rep1_S15",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR2-Rep1_S21",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR3-Rep1_S69",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF2-BinC-PCR4-Rep1_S75"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"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 SSFA2) 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": "2024-06-01T01:45:53.847312+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "0a89a59c-95d7-4ccf-a75d-9afb1d89d739"
}