{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4252ROMJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4252ROMJ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep1_S3",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep2_S58",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep1_S9",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep2_S64",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep1_S15",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep2_S70",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep1_S21",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep2_S76"
],
"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 [IGVFDS4252ROMJ](/auxiliary-sets/IGVFDS4252ROMJ/) has sequence file(s) [IGVFFI2043YWNR](/sequence-files/IGVFFI2043YWNR/), [IGVFFI4506MWVS](/sequence-files/IGVFFI4506MWVS/), [IGVFFI1890PKGY](/sequence-files/IGVFFI1890PKGY/), [IGVFFI7334BOPO](/sequence-files/IGVFFI7334BOPO/), [IGVFFI5042RRSN](/sequence-files/IGVFFI5042RRSN/), [IGVFFI9404PGPV](/sequence-files/IGVFFI9404PGPV/), [IGVFFI8568LLGQ](/sequence-files/IGVFFI8568LLGQ/), [IGVFFI0242VPKF](/sequence-files/IGVFFI0242VPKF/) 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/IGVFDS4252ROMJ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4252ROMJ](/auxiliary-sets/IGVFDS4252ROMJ/) 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/IGVFDS4252ROMJ/"
}
]
},
"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": "2024-05-21T17:12:24.271526+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/IGVFFI2043YWNR/",
"accession": "IGVFFI2043YWNR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep1_S3"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:07.482986+00:00",
"file_format": "fastq",
"file_size": 29091492,
"href": "/sequence-files/IGVFFI2043YWNR/@@download/IGVFFI2043YWNR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/94b4871a-039e-44be-ab8a-a38b161871f6/IGVFFI2043YWNR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinC-PCR1-Rep1_S3_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9392AVFW/",
"accession": "IGVFFI9392AVFW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep1_S3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:38.278134+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI9392AVFW/@@download/IGVFFI9392AVFW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/38c6ec98-dc25-4726-8c0d-0ff255f1c2c5/IGVFFI9392AVFW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinC-PCR1_Rep1_S3.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4506MWVS/",
"accession": "IGVFFI4506MWVS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep1_S9"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:47.307768+00:00",
"file_format": "fastq",
"file_size": 31581560,
"href": "/sequence-files/IGVFFI4506MWVS/@@download/IGVFFI4506MWVS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/171dffe0-1262-49e1-959e-67f1f00dcb25/IGVFFI4506MWVS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinC-PCR2-Rep1_S9_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1684INJA/",
"accession": "IGVFFI1684INJA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep2_S76"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:15.474540+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1684INJA/@@download/IGVFFI1684INJA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/bbf401da-1422-4b93-b714-cc6ab8c0f112/IGVFFI1684INJA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinC-PCR4_Rep2_S76.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1307DGAP/",
"accession": "IGVFFI1307DGAP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep1_S15"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:33.366697+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1307DGAP/@@download/IGVFFI1307DGAP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/ab047404-5d3e-4ed7-9fe9-20168098658b/IGVFFI1307DGAP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinC-PCR3_Rep1_S15.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1890PKGY/",
"accession": "IGVFFI1890PKGY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep2_S70"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:50.162677+00:00",
"file_format": "fastq",
"file_size": 13886933,
"href": "/sequence-files/IGVFFI1890PKGY/@@download/IGVFFI1890PKGY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/d45c17ab-36c2-4f67-a302-b9e4c35e2c5a/IGVFFI1890PKGY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinC-PCR3-Rep2_S70_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7410ZLTK/",
"accession": "IGVFFI7410ZLTK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep2_S58"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:51.658176+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI7410ZLTK/@@download/IGVFFI7410ZLTK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d8263e0b-50c8-43ec-a09f-9a576ff7543e/IGVFFI7410ZLTK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinC-PCR1_Rep2_S58.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7334BOPO/",
"accession": "IGVFFI7334BOPO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep2_S64"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:08.141080+00:00",
"file_format": "fastq",
"file_size": 19696273,
"href": "/sequence-files/IGVFFI7334BOPO/@@download/IGVFFI7334BOPO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b9e47f13-307c-40f2-8a66-445210d28c68/IGVFFI7334BOPO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinC-PCR2-Rep2_S64_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5042RRSN/",
"accession": "IGVFFI5042RRSN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep1_S15"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:28.834662+00:00",
"file_format": "fastq",
"file_size": 38727161,
"href": "/sequence-files/IGVFFI5042RRSN/@@download/IGVFFI5042RRSN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fa068516-1c71-4e72-ab59-1cb4640a43d7/IGVFFI5042RRSN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinC-PCR3-Rep1_S15_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9404PGPV/",
"accession": "IGVFFI9404PGPV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep2_S58"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:27.221922+00:00",
"file_format": "fastq",
"file_size": 9959917,
"href": "/sequence-files/IGVFFI9404PGPV/@@download/IGVFFI9404PGPV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c8af7250-ed35-494b-8dd6-c0870d2a1923/IGVFFI9404PGPV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8568LLGQ/",
"accession": "IGVFFI8568LLGQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep1_S21"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:10.335054+00:00",
"file_format": "fastq",
"file_size": 50825478,
"href": "/sequence-files/IGVFFI8568LLGQ/@@download/IGVFFI8568LLGQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/926a0a72-1ba5-495d-a365-b2aa27b1563e/IGVFFI8568LLGQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0242VPKF/",
"accession": "IGVFFI0242VPKF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep2_S76"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:30.708284+00:00",
"file_format": "fastq",
"file_size": 32226549,
"href": "/sequence-files/IGVFFI0242VPKF/@@download/IGVFFI0242VPKF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b4f4c96b-dd3b-4ead-94e3-78d75e146f65/IGVFFI0242VPKF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1001DNEG/",
"accession": "IGVFFI1001DNEG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep2_S70"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:47.575490+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1001DNEG/@@download/IGVFFI1001DNEG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2a96dad3-e1be-42f5-8569-48b331982192/IGVFFI1001DNEG.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7786EDHN/",
"accession": "IGVFFI7786EDHN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep2_S64"
],
"content_type": "seqspec",
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"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI7786EDHN/@@download/IGVFFI7786EDHN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8d9844f1-4470-4637-a6bd-8f4e3fc77b75/IGVFFI7786EDHN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinC-PCR2_Rep2_S64.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7398OLMO/",
"accession": "IGVFFI7398OLMO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep1_S9"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI7398OLMO/@@download/IGVFFI7398OLMO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/56e57d7a-4a60-4883-ad06-1e387f26ecff/IGVFFI7398OLMO.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinC-PCR2_Rep1_S9.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8293WPGQ/",
"accession": "IGVFFI8293WPGQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep1_S21"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:01.510823+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI8293WPGQ/@@download/IGVFFI8293WPGQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0dc6cd41-b385-4d83-b46a-524223ed50f8/IGVFFI8293WPGQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinC-PCR4_Rep1_S21.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1310KDLX/",
"accession": "IGVFDS1310KDLX",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep1_S3",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep2_S58",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep1_S9",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep2_S64",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep1_S15",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep2_S70",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep1_S21",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep2_S76"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:19:29.095374+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4577TQPO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4577TQPO",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep1_S3",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR1_Rep2_S58",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep1_S9",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR2_Rep2_S64",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep1_S15",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR3_Rep2_S70",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep1_S21",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinC-PCR4_Rep2_S76"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"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 C for 35-45% expression of MYC) 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": "2024-06-01T01:58:07.482986+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "08ad8bf0-4cca-4e4b-bf4d-c76b4533a08b"
}