{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4902IYAA/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4902IYAA",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3721QHDS](/in-vitro-systems/IGVFSM3721QHDS/) 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/IGVFSM3721QHDS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3721QHDS](/in-vitro-systems/IGVFSM3721QHDS/) 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/IGVFSM3721QHDS/"
},
{
"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 [IGVFDS4902IYAA](/auxiliary-sets/IGVFDS4902IYAA/) has sequence file(s) [IGVFFI0996XOGX](/sequence-files/IGVFFI0996XOGX/), [IGVFFI5866ZGPN](/sequence-files/IGVFFI5866ZGPN/), [IGVFFI5619AUER](/sequence-files/IGVFFI5619AUER/), [IGVFFI4198FZCC](/sequence-files/IGVFFI4198FZCC/) 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/IGVFDS4902IYAA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4902IYAA](/auxiliary-sets/IGVFDS4902IYAA/) 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/IGVFDS4902IYAA/"
}
]
},
"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": "2024-05-13T22:50:48.467880+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/IGVFFI0996XOGX/",
"accession": "IGVFFI0996XOGX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:12.473543+00:00",
"file_format": "fastq",
"file_size": 15063113,
"href": "/sequence-files/IGVFFI0996XOGX/@@download/IGVFFI0996XOGX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e86ccab8-6f69-4988-943c-1b657b3ef908/IGVFFI0996XOGX.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-BinE-PCR1-Rep1_S245_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4801IXZV/",
"accession": "IGVFFI4801IXZV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:01.506095+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI4801IXZV/@@download/IGVFFI4801IXZV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/24b933e6-c98b-44b8-be78-9394f6f6d788/IGVFFI4801IXZV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5866ZGPN/",
"accession": "IGVFFI5866ZGPN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:29.854353+00:00",
"file_format": "fastq",
"file_size": 13911957,
"href": "/sequence-files/IGVFFI5866ZGPN/@@download/IGVFFI5866ZGPN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/cf0558d7-5a5b-4990-9754-770c102dd8a5/IGVFFI5866ZGPN.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-BinE-PCR2-Rep1_S251_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5619AUER/",
"accession": "IGVFFI5619AUER",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:42:46.956510+00:00",
"file_format": "fastq",
"file_size": 25749453,
"href": "/sequence-files/IGVFFI5619AUER/@@download/IGVFFI5619AUER.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0353b05e-c812-4aee-8d5d-3e2f9ef1a3cf/IGVFFI5619AUER.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-BinE-PCR3-Rep1_S287_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4198FZCC/",
"accession": "IGVFFI4198FZCC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:43:06.764177+00:00",
"file_format": "fastq",
"file_size": 20814259,
"href": "/sequence-files/IGVFFI4198FZCC/@@download/IGVFFI4198FZCC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7e0aaf75-9c01-4a0b-a7de-166b8da6c731/IGVFFI4198FZCC.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-BinE-PCR4-Rep1_S293_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8151RHFP/",
"accession": "IGVFFI8151RHFP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:44.206699+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI8151RHFP/@@download/IGVFFI8151RHFP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/750fa75e-922b-4f5a-8578-f6b0cee7e1f8/IGVFFI8151RHFP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9366NHKY/",
"accession": "IGVFFI9366NHKY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:29.677954+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9366NHKY/@@download/IGVFFI9366NHKY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/71ee6ac3-ae7c-492e-b60c-98c1fbd4ca57/IGVFFI9366NHKY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4206WEWP/",
"accession": "IGVFFI4206WEWP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:15.655945+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI4206WEWP/@@download/IGVFFI4206WEWP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f878d2ac-d0c5-430e-b663-7fe52af847f3/IGVFFI4206WEWP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2368HJNA/",
"accession": "IGVFDS2368HJNA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:09:40.781041+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3721QHDS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3721QHDS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR1-Rep1_S245",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR2-Rep1_S251",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR3-Rep1_S287",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinE-PCR4-Rep1_S293"
],
"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 E for 80-90% 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": "2024-06-01T01:42:12.473543+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "81ca09ea-3d5a-4e32-9903-21cf4c1c1007"
}