{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0993NTCB/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0993NTCB",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
],
"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 [IGVFDS0993NTCB](/auxiliary-sets/IGVFDS0993NTCB/) has sequence file(s) [IGVFFI7894YYZC](/sequence-files/IGVFFI7894YYZC/), [IGVFFI8705DNZH](/sequence-files/IGVFFI8705DNZH/), [IGVFFI7395GMMQ](/sequence-files/IGVFFI7395GMMQ/), [IGVFFI9082ISDE](/sequence-files/IGVFFI9082ISDE/) 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/IGVFDS0993NTCB/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0993NTCB](/auxiliary-sets/IGVFDS0993NTCB/) 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/IGVFDS0993NTCB/"
}
]
},
"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": "2024-05-14T16:24:22.975926+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/IGVFFI7894YYZC/",
"accession": "IGVFFI7894YYZC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:19.148644+00:00",
"file_format": "fastq",
"file_size": 24225395,
"href": "/sequence-files/IGVFFI7894YYZC/@@download/IGVFFI7894YYZC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a7cf7146-d4c5-46ea-a908-a39386bf4ca5/IGVFFI7894YYZC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinE-PCR1-Rep1_S125_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1274LNCV/",
"accession": "IGVFFI1274LNCV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:55.331019+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI1274LNCV/@@download/IGVFFI1274LNCV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f41132e6-e0e9-4d18-86e1-fba82ddfd04f/IGVFFI1274LNCV.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8705DNZH/",
"accession": "IGVFFI8705DNZH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:37.012660+00:00",
"file_format": "fastq",
"file_size": 23951492,
"href": "/sequence-files/IGVFFI8705DNZH/@@download/IGVFFI8705DNZH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b80efc39-d524-447c-8855-6e8ca0eaf051/IGVFFI8705DNZH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinE-PCR2-Rep1_S131_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7395GMMQ/",
"accession": "IGVFFI7395GMMQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:55.384991+00:00",
"file_format": "fastq",
"file_size": 31056667,
"href": "/sequence-files/IGVFFI7395GMMQ/@@download/IGVFFI7395GMMQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0e0794bf-c0fa-48ff-a40b-89450e6efbf3/IGVFFI7395GMMQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinE-PCR3-Rep1_S179_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9082ISDE/",
"accession": "IGVFFI9082ISDE",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:13.412020+00:00",
"file_format": "fastq",
"file_size": 30206781,
"href": "/sequence-files/IGVFFI9082ISDE/@@download/IGVFFI9082ISDE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f61fa0f0-dbf2-4685-9ef8-1f2f194b96af/IGVFFI9082ISDE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinE-PCR4-Rep1_S185_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5302WHBP/",
"accession": "IGVFFI5302WHBP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:36.562343+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI5302WHBP/@@download/IGVFFI5302WHBP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/99b249a3-f56c-445d-950d-2c9e68751acd/IGVFFI5302WHBP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5240ILIB/",
"accession": "IGVFFI5240ILIB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:23.243379+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI5240ILIB/@@download/IGVFFI5240ILIB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/eeface6f-90f4-4ff4-9adb-d56ebd7199b9/IGVFFI5240ILIB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3040ASPY/",
"accession": "IGVFFI3040ASPY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:09.120633+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI3040ASPY/@@download/IGVFFI3040ASPY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b162e737-2412-4b42-899b-389f4901a51f/IGVFFI3040ASPY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6734DXEE/",
"accession": "IGVFDS6734DXEE",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:11:50.093856+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1344KAZA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1344KAZA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR1-Rep1_S125",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR2-Rep1_S131",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR3-Rep1_S179",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinE-PCR4-Rep1_S185"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"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 FAM3C) 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": "2024-06-01T01:52:19.148644+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "bf7513b2-7b56-4eee-b670-14b647e3735b"
}