{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6449NYRM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6449NYRM",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
],
"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 [IGVFDS6449NYRM](/auxiliary-sets/IGVFDS6449NYRM/) has sequence file(s) [IGVFFI5340ERRF](/sequence-files/IGVFFI5340ERRF/), [IGVFFI3781TWXY](/sequence-files/IGVFFI3781TWXY/), [IGVFFI7194FCZO](/sequence-files/IGVFFI7194FCZO/), [IGVFFI5756XBGF](/sequence-files/IGVFFI5756XBGF/) 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/IGVFDS6449NYRM/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6449NYRM](/auxiliary-sets/IGVFDS6449NYRM/) 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/IGVFDS6449NYRM/"
}
]
},
"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": "2024-05-14T16:23:50.611222+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/IGVFFI5340ERRF/",
"accession": "IGVFFI5340ERRF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:50:53.033706+00:00",
"file_format": "fastq",
"file_size": 29645689,
"href": "/sequence-files/IGVFFI5340ERRF/@@download/IGVFFI5340ERRF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b2be5530-e578-4e63-aa88-2a3336957ba3/IGVFFI5340ERRF.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-BinB-PCR1-Rep1_S110_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8839AZBX/",
"accession": "IGVFFI8839AZBX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:41:51.907765+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI8839AZBX/@@download/IGVFFI8839AZBX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c4bb3e42-d746-4b1a-9dd4-8fb2b84c8773/IGVFFI8839AZBX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3781TWXY/",
"accession": "IGVFFI3781TWXY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:13.343746+00:00",
"file_format": "fastq",
"file_size": 17142969,
"href": "/sequence-files/IGVFFI3781TWXY/@@download/IGVFFI3781TWXY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/63935fca-4d4d-47c0-a3b7-4428efb9fc41/IGVFFI3781TWXY.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-BinB-PCR2-Rep1_S116_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7194FCZO/",
"accession": "IGVFFI7194FCZO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:31.659015+00:00",
"file_format": "fastq",
"file_size": 33809110,
"href": "/sequence-files/IGVFFI7194FCZO/@@download/IGVFFI7194FCZO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/8b4e27a1-caf4-4d02-b66a-1c7e5db9772f/IGVFFI7194FCZO.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-BinB-PCR3-Rep1_S164_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5756XBGF/",
"accession": "IGVFFI5756XBGF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:51:51.214330+00:00",
"file_format": "fastq",
"file_size": 25935699,
"href": "/sequence-files/IGVFFI5756XBGF/@@download/IGVFFI5756XBGF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/17415866-bf69-449f-8b96-ad863438e9c1/IGVFFI5756XBGF.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-BinB-PCR4-Rep1_S170_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3497STEU/",
"accession": "IGVFFI3497STEU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:35.238532+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI3497STEU/@@download/IGVFFI3497STEU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/331ed763-685b-45ff-9c1f-922f1f7f5a5c/IGVFFI3497STEU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6612QXQL/",
"accession": "IGVFFI6612QXQL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:07.386375+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI6612QXQL/@@download/IGVFFI6612QXQL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f110eaf1-dfaf-4174-9b83-e2e5ce637ccd/IGVFFI6612QXQL.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2959DQXK/",
"accession": "IGVFFI2959DQXK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:22.189814+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI2959DQXK/@@download/IGVFFI2959DQXK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3a95b09e-8aa1-4892-8d8b-08aa1f2fb77d/IGVFFI2959DQXK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6704KMTH/",
"accession": "IGVFDS6704KMTH",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:10:45.555140+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0069TVXJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0069TVXJ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR1-Rep1_S110",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR2-Rep1_S116",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR3-Rep1_S164",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF1-BinB-PCR4-Rep1_S170"
],
"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 B for 10-20% 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": "2024-06-01T01:50:53.033706+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "60782528-957f-4783-b0ce-6cf44a347685"
}