{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2084ZSSG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2084ZSSG",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
],
"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 [IGVFSM7718ZYYQ](/in-vitro-systems/IGVFSM7718ZYYQ/) 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/IGVFSM7718ZYYQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7718ZYYQ](/in-vitro-systems/IGVFSM7718ZYYQ/) 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/IGVFSM7718ZYYQ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2084ZSSG](/auxiliary-sets/IGVFDS2084ZSSG/) has sequence file(s) [IGVFFI0753QNVY](/sequence-files/IGVFFI0753QNVY/), [IGVFFI8888QXML](/sequence-files/IGVFFI8888QXML/), [IGVFFI9575XKJG](/sequence-files/IGVFFI9575XKJG/), [IGVFFI3313PFDP](/sequence-files/IGVFFI3313PFDP/) 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/IGVFDS2084ZSSG/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2084ZSSG](/auxiliary-sets/IGVFDS2084ZSSG/) 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/IGVFDS2084ZSSG/"
}
]
},
"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": "2024-05-13T22:50:49.539613+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/IGVFFI0753QNVY/",
"accession": "IGVFFI0753QNVY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:15.781055+00:00",
"file_format": "fastq",
"file_size": 19663507,
"href": "/sequence-files/IGVFFI0753QNVY/@@download/IGVFFI0753QNVY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c19e57b0-db9c-490c-901a-865a636575cf/IGVFFI0753QNVY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinF-PCR1-Rep1_S246_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8908XMQK/",
"accession": "IGVFFI8908XMQK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:04.028101+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI8908XMQK/@@download/IGVFFI8908XMQK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b5efd564-73cf-4d58-88d1-d3d51b6b7fb3/IGVFFI8908XMQK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8888QXML/",
"accession": "IGVFFI8888QXML",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:32.556190+00:00",
"file_format": "fastq",
"file_size": 14562870,
"href": "/sequence-files/IGVFFI8888QXML/@@download/IGVFFI8888QXML.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/49882cd5-7113-4362-9fcc-7836a8a2749e/IGVFFI8888QXML.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinF-PCR2-Rep1_S252_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9575XKJG/",
"accession": "IGVFFI9575XKJG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:49.899464+00:00",
"file_format": "fastq",
"file_size": 29442591,
"href": "/sequence-files/IGVFFI9575XKJG/@@download/IGVFFI9575XKJG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6d3d5fb9-ef30-47a2-a7e8-d7271c939b28/IGVFFI9575XKJG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinF-PCR3-Rep1_S288_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3313PFDP/",
"accession": "IGVFFI3313PFDP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:09.564609+00:00",
"file_format": "fastq",
"file_size": 31736889,
"href": "/sequence-files/IGVFFI3313PFDP/@@download/IGVFFI3313PFDP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b9964b31-efcb-422b-a903-bcefaa5b618c/IGVFFI3313PFDP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinF-PCR4-Rep1_S294_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1849NKLD/",
"accession": "IGVFFI1849NKLD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:31.954015+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1849NKLD/@@download/IGVFFI1849NKLD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8c0f735a-d7bf-431c-a2ec-a52f1ad6e85e/IGVFFI1849NKLD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5842FKDB/",
"accession": "IGVFFI5842FKDB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:46.473880+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5842FKDB/@@download/IGVFFI5842FKDB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5c937862-0e7c-4982-afd3-6b76ad509d16/IGVFFI5842FKDB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4334FUHO/",
"accession": "IGVFFI4334FUHO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:17.908462+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4334FUHO/@@download/IGVFFI4334FUHO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a7507ebf-4907-4e25-ba1c-bf5c51b0fae9/IGVFFI4334FUHO.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5981KTQT/",
"accession": "IGVFDS5981KTQT",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:09:48.647256+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7718ZYYQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7718ZYYQ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR1-Rep1_S246",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR2-Rep1_S252",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR3-Rep1_S288",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinF-PCR4-Rep1_S294"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"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 CCND1) 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": "2024-06-01T01:42:15.781055+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "66935e00-cc32-403c-9112-afda3a65e0d0"
}