{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6919SLGV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6919SLGV",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR1-Rep1_S42",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR2-Rep1_S48",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR3-Rep1_S96",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR4-Rep1_S102"
],
"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/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8591NYNI](/in-vitro-systems/IGVFSM8591NYNI/) has in progress subobject degron modification [95081d1b-08b4-49ed-b324-e53fc43d8456](/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8591NYNI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8591NYNI](/in-vitro-systems/IGVFSM8591NYNI/) has in progress subobject treatment [d35868d1-c45b-49ae-8ff3-a9c0c22551c2](/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8591NYNI/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6919SLGV](/auxiliary-sets/IGVFDS6919SLGV/) has sequence file(s) [IGVFFI4812DJTV](/sequence-files/IGVFFI4812DJTV/), [IGVFFI3535RDKO](/sequence-files/IGVFFI3535RDKO/), [IGVFFI8079ESYV](/sequence-files/IGVFFI8079ESYV/), [IGVFFI0793MEHU](/sequence-files/IGVFFI0793MEHU/) 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/IGVFDS6919SLGV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6919SLGV](/auxiliary-sets/IGVFDS6919SLGV/) 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/IGVFDS6919SLGV/"
}
]
},
"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": "2024-05-14T21:06:47.802694+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/IGVFFI4812DJTV/",
"accession": "IGVFFI4812DJTV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR1-Rep1_S42"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:48:33.099297+00:00",
"file_format": "fastq",
"file_size": 15313538,
"href": "/sequence-files/IGVFFI4812DJTV/@@download/IGVFFI4812DJTV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/74f1adc1-04dd-4dac-8b8f-a7f73c35d285/IGVFFI4812DJTV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinF-PCR1-Rep1_S42_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1091GUCU/",
"accession": "IGVFFI1091GUCU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR1-Rep1_S42"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:40:58.247040+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI1091GUCU/@@download/IGVFFI1091GUCU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a693f542-2c4f-494f-84ef-4f3eedc38b4f/IGVFFI1091GUCU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinF-PCR1-Rep1_S42.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3535RDKO/",
"accession": "IGVFFI3535RDKO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR3-Rep1_S96"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:49:08.186848+00:00",
"file_format": "fastq",
"file_size": 24259657,
"href": "/sequence-files/IGVFFI3535RDKO/@@download/IGVFFI3535RDKO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a7af0036-4f1e-40e1-85e8-3af9806a2187/IGVFFI3535RDKO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinF-PCR3-Rep1_S96_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2878TVWP/",
"accession": "IGVFFI2878TVWP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR2-Rep1_S48"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:14.242157+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2878TVWP/@@download/IGVFFI2878TVWP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/16807763-cbdf-4736-8113-a805c675c458/IGVFFI2878TVWP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinF-PCR2-Rep1_S48.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8079ESYV/",
"accession": "IGVFFI8079ESYV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR2-Rep1_S48"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:48:50.331244+00:00",
"file_format": "fastq",
"file_size": 652652,
"href": "/sequence-files/IGVFFI8079ESYV/@@download/IGVFFI8079ESYV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b83718fc-b069-45b0-9d75-76be9cea12f6/IGVFFI8079ESYV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinF-PCR2-Rep1_S48_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0793MEHU/",
"accession": "IGVFFI0793MEHU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR4-Rep1_S102"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:49:26.785020+00:00",
"file_format": "fastq",
"file_size": 1321840,
"href": "/sequence-files/IGVFFI0793MEHU/@@download/IGVFFI0793MEHU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2bbbcf82-fa54-428e-92dd-ce1ffc9b5a9c/IGVFFI0793MEHU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/SSFA2-Auxin6hrs-FF2-BinF-PCR4-Rep1_S102_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4911SPHY/",
"accession": "IGVFFI4911SPHY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR3-Rep1_S96"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:29.728987+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4911SPHY/@@download/IGVFFI4911SPHY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7bbe52d8-97e3-4a51-8b5f-7592ba1a2741/IGVFFI4911SPHY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinF-PCR3-Rep1_S96.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8669XCXT/",
"accession": "IGVFFI8669XCXT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR4-Rep1_S102"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:45.253166+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8669XCXT/@@download/IGVFFI8669XCXT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a9577207-6f3e-45f8-9f0e-b7190aa1829a/IGVFFI8669XCXT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin6hrs-FF2-BinF-PCR4-Rep1_S102.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1436SBBU/",
"accession": "IGVFDS1436SBBU",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR1-Rep1_S42",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR2-Rep1_S48",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR3-Rep1_S96",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR4-Rep1_S102"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:26:27.691648+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8591NYNI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8591NYNI",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR1-Rep1_S42",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR2-Rep1_S48",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR3-Rep1_S96",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin6hrs-FF2-BinF-PCR4-Rep1_S102"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5413RKIA/"
],
"modifications": [
"/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"/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 F for 80-100% expression of SSFA2) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with a guide library",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/"
]
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:48:33.099297+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "91bbe122-713b-47bb-9d84-2f7465e3cc18"
}