{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8896GBSX/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8896GBSX",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
"jesse-engreitz:auxiliary_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8896GBSX](/auxiliary-sets/IGVFDS8896GBSX/) has sequence file(s) [IGVFFI7202YFCO](/sequence-files/IGVFFI7202YFCO/), [IGVFFI6253BEMU](/sequence-files/IGVFFI6253BEMU/), [IGVFFI8588OWHR](/sequence-files/IGVFFI8588OWHR/), [IGVFFI4477VBFK](/sequence-files/IGVFFI4477VBFK/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8896GBSX/"
}
]
},
"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": "2024-05-06T23:13:29.862972+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/IGVFFI7202YFCO/",
"accession": "IGVFFI7202YFCO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:24:49.779269+00:00",
"file_format": "fastq",
"file_size": 8029659,
"href": "/sequence-files/IGVFFI7202YFCO/@@download/IGVFFI7202YFCO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/81a01701-ddd1-408e-91e2-161a83839c43/IGVFFI7202YFCO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinE-PCR1_S5_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7049RBOE/",
"accession": "IGVFFI7049RBOE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:02.927893+00:00",
"file_format": "yaml",
"file_size": 907,
"href": "/configuration-files/IGVFFI7049RBOE/@@download/IGVFFI7049RBOE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/04c8eb81-090d-463c-b168-f358c1a7b924/IGVFFI7049RBOE.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinE-PCR1_S5.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6253BEMU/",
"accession": "IGVFFI6253BEMU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:05.966807+00:00",
"file_format": "fastq",
"file_size": 9936331,
"href": "/sequence-files/IGVFFI6253BEMU/@@download/IGVFFI6253BEMU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e77e9328-4b72-44fe-8077-bc8e8e55943f/IGVFFI6253BEMU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinE-PCR2_S101_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8588OWHR/",
"accession": "IGVFFI8588OWHR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:22.135544+00:00",
"file_format": "fastq",
"file_size": 10927968,
"href": "/sequence-files/IGVFFI8588OWHR/@@download/IGVFFI8588OWHR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/384f4a21-e899-4834-96a3-ab7edd43fa7c/IGVFFI8588OWHR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinE-PCR3_S197_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4477VBFK/",
"accession": "IGVFFI4477VBFK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:25:37.661835+00:00",
"file_format": "fastq",
"file_size": 9242968,
"href": "/sequence-files/IGVFFI4477VBFK/@@download/IGVFFI4477VBFK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d27d9ec6-5f48-483c-9a13-2019b1212841/IGVFFI4477VBFK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/210301B002-CohesinFF/fastq/CCND1-Auxin6hrs-FF1-BinE-PCR4_S293_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0941NMED/",
"accession": "IGVFFI0941NMED",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:16.658108+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI0941NMED/@@download/IGVFFI0941NMED.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a07c260b-b450-42b7-b6cb-2b6cecb81d8d/IGVFFI0941NMED.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinE-PCR2_S101.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6010EIDV/",
"accession": "IGVFFI6010EIDV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:43.857769+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI6010EIDV/@@download/IGVFFI6010EIDV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b1a199cf-ff53-4e09-afdf-2bed65722129/IGVFFI6010EIDV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinE-PCR4_S293.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2066FCAJ/",
"accession": "IGVFFI2066FCAJ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:23:30.205187+00:00",
"file_format": "yaml",
"file_size": 908,
"href": "/configuration-files/IGVFFI2066FCAJ/@@download/IGVFFI2066FCAJ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9b74f33e-7d2b-4d0c-ace4-a5592eeab6b7/IGVFFI2066FCAJ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1-Auxin6hrs-FF1-BinE-PCR3_S197.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2982SJGW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3802XLBV/",
"accession": "IGVFDS3802XLBV",
"aliases": [
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
"jesse-engreitz:measurement_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:23:27.362746+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9116DXLY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9116DXLY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR1_S5",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR2_S101",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR3_S197",
"jesse-engreitz:in-vitro-system_CRUDO_PILOT_CCND1-Auxin6hrs-FF1-BinE-PCR4_S293"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0392OWNZ/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"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 E for 80-90% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:24:49.779269+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in 36 genomic loci",
"uuid": "1d76ab28-b9b6-41b6-a47b-969e2ceb0f68"
}