{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6282WCIA/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6282WCIA",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
],
"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 [IGVFDS6282WCIA](/auxiliary-sets/IGVFDS6282WCIA/) has sequence file(s) [IGVFFI4637QKGZ](/sequence-files/IGVFFI4637QKGZ/), [IGVFFI6534BXXG](/sequence-files/IGVFFI6534BXXG/), [IGVFFI4232HLWS](/sequence-files/IGVFFI4232HLWS/), [IGVFFI2737UPLU](/sequence-files/IGVFFI2737UPLU/) 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/IGVFDS6282WCIA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6282WCIA](/auxiliary-sets/IGVFDS6282WCIA/) 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/IGVFDS6282WCIA/"
}
]
},
"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": "2024-05-13T22:39:16.530545+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/IGVFFI4637QKGZ/",
"accession": "IGVFFI4637QKGZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:20.701469+00:00",
"file_format": "fastq",
"file_size": 29405205,
"href": "/sequence-files/IGVFFI4637QKGZ/@@download/IGVFFI4637QKGZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/042cff1c-f9c7-401c-974a-da3664b59376/IGVFFI4637QKGZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinE-PCR1-Rep1_S233_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2698LUYO/",
"accession": "IGVFFI2698LUYO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:05.800223+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI2698LUYO/@@download/IGVFFI2698LUYO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ef796ab8-5ea9-422b-a850-e2c16801d071/IGVFFI2698LUYO.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6534BXXG/",
"accession": "IGVFFI6534BXXG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:38.303413+00:00",
"file_format": "fastq",
"file_size": 18504941,
"href": "/sequence-files/IGVFFI6534BXXG/@@download/IGVFFI6534BXXG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/01fa316e-8746-4183-a0e7-273f62338de0/IGVFFI6534BXXG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinE-PCR2-Rep1_S239_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4232HLWS/",
"accession": "IGVFFI4232HLWS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:37:55.962582+00:00",
"file_format": "fastq",
"file_size": 32150955,
"href": "/sequence-files/IGVFFI4232HLWS/@@download/IGVFFI4232HLWS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/27886f37-a435-4b71-aef5-161328022c2f/IGVFFI4232HLWS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinE-PCR3-Rep1_S275_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2737UPLU/",
"accession": "IGVFFI2737UPLU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:41:54.276520+00:00",
"file_format": "fastq",
"file_size": 25032339,
"href": "/sequence-files/IGVFFI2737UPLU/@@download/IGVFFI2737UPLU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/57d4bcbf-ea4b-48f6-9150-75785f0cb55c/IGVFFI2737UPLU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin0hrs-FF2-BinE-PCR4-Rep1_S281_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0884PTAR/",
"accession": "IGVFFI0884PTAR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:19.605413+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI0884PTAR/@@download/IGVFFI0884PTAR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/de333ec7-d958-436a-b0d8-0c82fed01d5f/IGVFFI0884PTAR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9590CNGN/",
"accession": "IGVFFI9590CNGN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:47.582235+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9590CNGN/@@download/IGVFFI9590CNGN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f3398629-3486-42ce-b5b9-de96d7aeb7ee/IGVFFI9590CNGN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2548FNWF/",
"accession": "IGVFFI2548FNWF",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:33.621814+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2548FNWF/@@download/IGVFFI2548FNWF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a6755d98-3357-407d-a32d-4a52f2c931c2/IGVFFI2548FNWF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5565SKCZ/",
"accession": "IGVFDS5565SKCZ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"notes": "The origninal alias jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S2817 was changed to jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281",
"release_timestamp": "2024-07-10T20:08:57.462015+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0671URTU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0671URTU",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR1-Rep1_S233",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR2-Rep1_S239",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR3-Rep1_S275",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF2-BinE-PCR4-Rep1_S281"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"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 E for 80-90% expression of CCND1) 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": "2024-06-01T01:37:20.701469+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "79e0557f-59bb-4aa4-84ae-6d33041f3996"
}