{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4433BYLP/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4433BYLP",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR1-Rep1_S112",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR2-Rep1_S118",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR3-Rep1_S166",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR4-Rep1_S172"
],
"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 [IGVFDS4433BYLP](/auxiliary-sets/IGVFDS4433BYLP/) has sequence file(s) [IGVFFI2710BHTW](/sequence-files/IGVFFI2710BHTW/), [IGVFFI7846ILRU](/sequence-files/IGVFFI7846ILRU/), [IGVFFI5205NSJU](/sequence-files/IGVFFI5205NSJU/), [IGVFFI2058BHVX](/sequence-files/IGVFFI2058BHVX/) 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/IGVFDS4433BYLP/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4433BYLP](/auxiliary-sets/IGVFDS4433BYLP/) 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/IGVFDS4433BYLP/"
}
]
},
"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": "2024-05-14T16:23:53.500865+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/IGVFFI2710BHTW/",
"accession": "IGVFFI2710BHTW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR1-Rep1_S112"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:50:59.190148+00:00",
"file_format": "fastq",
"file_size": 24638761,
"href": "/sequence-files/IGVFFI2710BHTW/@@download/IGVFFI2710BHTW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0e790860-ba73-472b-bb46-8dba3b8807cb/IGVFFI2710BHTW.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-FF1-BinD-PCR1-Rep1_S112_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1251FATT/",
"accession": "IGVFFI1251FATT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR1-Rep1_S112"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:57.296968+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1251FATT/@@download/IGVFFI1251FATT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/595d91a4-fbd2-4b16-ad8c-dbfba5b1fee4/IGVFFI1251FATT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinD-PCR1-Rep1_S112.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7846ILRU/",
"accession": "IGVFFI7846ILRU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR2-Rep1_S118"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:19.536034+00:00",
"file_format": "fastq",
"file_size": 27527978,
"href": "/sequence-files/IGVFFI7846ILRU/@@download/IGVFFI7846ILRU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5c43baed-3ef9-425f-8053-410c1c7606ff/IGVFFI7846ILRU.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-FF1-BinD-PCR2-Rep1_S118_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5205NSJU/",
"accession": "IGVFFI5205NSJU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR3-Rep1_S166"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:37.601123+00:00",
"file_format": "fastq",
"file_size": 34188374,
"href": "/sequence-files/IGVFFI5205NSJU/@@download/IGVFFI5205NSJU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/4add2170-c541-40bd-97cf-91e3c3abe5c5/IGVFFI5205NSJU.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-FF1-BinD-PCR3-Rep1_S166_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2058BHVX/",
"accession": "IGVFFI2058BHVX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR4-Rep1_S172"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:57.364245+00:00",
"file_format": "fastq",
"file_size": 36289524,
"href": "/sequence-files/IGVFFI2058BHVX/@@download/IGVFFI2058BHVX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ac54391b-def8-4acb-aa8e-d1cd9a5a2cec/IGVFFI2058BHVX.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-FF1-BinD-PCR4-Rep1_S172_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2393MWOU/",
"accession": "IGVFFI2393MWOU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR3-Rep1_S166"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:26.398393+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI2393MWOU/@@download/IGVFFI2393MWOU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c993e4ff-92d7-4cf4-b786-517e69d340a5/IGVFFI2393MWOU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinD-PCR3-Rep1_S166.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3111HNUW/",
"accession": "IGVFFI3111HNUW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR4-Rep1_S172"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:39.781573+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI3111HNUW/@@download/IGVFFI3111HNUW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/87f5fd9e-245b-4071-9f85-b84eae6b8e9d/IGVFFI3111HNUW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinD-PCR4-Rep1_S172.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8401XSSD/",
"accession": "IGVFFI8401XSSD",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR2-Rep1_S118"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:12.465915+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI8401XSSD/@@download/IGVFFI8401XSSD.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6a58cfff-5749-47df-9735-59c35db4f652/IGVFFI8401XSSD.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinD-PCR2-Rep1_S118.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6273UIFG/",
"accession": "IGVFDS6273UIFG",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR1-Rep1_S112",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR2-Rep1_S118",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR3-Rep1_S166",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR4-Rep1_S172"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:10:59.848791+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7317UFYW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7317UFYW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR1-Rep1_S112",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR2-Rep1_S118",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR3-Rep1_S166",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinD-PCR4-Rep1_S172"
],
"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 D for 55-65% 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": "2024-06-01T01:50:59.190148+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a58f116a-2905-4b52-8caa-06171acfaf54"
}