{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4701YCEL/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4701YCEL",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep1_S2",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep2_S57",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep1_S8",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep2_S63",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR3_Rep1_S14",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR3_Rep2_S69",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR4_Rep1_S20",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR4_Rep2_S75"
],
"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 [IGVFDS4701YCEL](/auxiliary-sets/IGVFDS4701YCEL/) has sequence file(s) [IGVFFI6952RHQM](/sequence-files/IGVFFI6952RHQM/), [IGVFFI1122HKWU](/sequence-files/IGVFFI1122HKWU/), [IGVFFI1697DZHB](/sequence-files/IGVFFI1697DZHB/), [IGVFFI8224NGZQ](/sequence-files/IGVFFI8224NGZQ/), [IGVFFI7565VCLO](/sequence-files/IGVFFI7565VCLO/), [IGVFFI3742WWYT](/sequence-files/IGVFFI3742WWYT/), [IGVFFI7880EKFD](/sequence-files/IGVFFI7880EKFD/), [IGVFFI1267BFAZ](/sequence-files/IGVFFI1267BFAZ/) 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/IGVFDS4701YCEL/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4701YCEL](/auxiliary-sets/IGVFDS4701YCEL/) 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/IGVFDS4701YCEL/"
}
]
},
"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": "2024-05-21T17:12:23.160528+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",
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{
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"accession": "IGVFFI6952RHQM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep1_S2"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 26576571,
"href": "/sequence-files/IGVFFI6952RHQM/@@download/IGVFFI6952RHQM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/211edaa7-2f35-45de-b658-f48f2fc815f4/IGVFFI6952RHQM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1477HXVA/",
"accession": "IGVFFI1477HXVA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep1_S2"
],
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"creation_timestamp": "2024-06-11T20:45:36.072436+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1477HXVA/@@download/IGVFFI1477HXVA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/80a9f263-7945-4bdd-8bd5-b0e4d64b184a/IGVFFI1477HXVA.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1122HKWU/",
"accession": "IGVFFI1122HKWU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep2_S63"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:03.480924+00:00",
"file_format": "fastq",
"file_size": 16680646,
"href": "/sequence-files/IGVFFI1122HKWU/@@download/IGVFFI1122HKWU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6a5362d6-81e8-458f-87fd-7388c46169db/IGVFFI1122HKWU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinB-PCR2-Rep2_S63_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1697DZHB/",
"accession": "IGVFFI1697DZHB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep2_S57"
],
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"file_size": 18226364,
"href": "/sequence-files/IGVFFI1697DZHB/@@download/IGVFFI1697DZHB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/dca9890a-b734-4971-b6d5-5d762437d6c3/IGVFFI1697DZHB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinB-PCR1-Rep2_S57_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8224NGZQ/",
"accession": "IGVFFI8224NGZQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR4_Rep2_S75"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:27.034382+00:00",
"file_format": "fastq",
"file_size": 21449241,
"href": "/sequence-files/IGVFFI8224NGZQ/@@download/IGVFFI8224NGZQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2bd122dd-7ca4-4426-9c19-0b7669fbbe0d/IGVFFI8224NGZQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinB-PCR4-Rep2_S75_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7757NDSP/",
"accession": "IGVFFI7757NDSP",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep1_S8"
],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI7757NDSP/@@download/IGVFFI7757NDSP.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/42a728ea-5e96-448a-a908-48dbad63a2cf/IGVFFI7757NDSP.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinB-PCR2_Rep1_S8.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4681EQRI/",
"accession": "IGVFFI4681EQRI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR4_Rep2_S75"
],
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"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI4681EQRI/@@download/IGVFFI4681EQRI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0ae9bb3b-4b30-43d1-b936-d8b3cda369c9/IGVFFI4681EQRI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinB-PCR4_Rep2_S75.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7565VCLO/",
"accession": "IGVFFI7565VCLO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep1_S8"
],
"content_type": "reads",
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"href": "/sequence-files/IGVFFI7565VCLO/@@download/IGVFFI7565VCLO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f27a0f8e-cf26-41d4-9d6f-67682142441d/IGVFFI7565VCLO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3742WWYT/",
"accession": "IGVFFI3742WWYT",
"aliases": [
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],
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"s3_uri": "s3://igvf-files/2024/06/01/357c8ac4-66e4-416f-b015-6503b2ec77c7/IGVFFI3742WWYT.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7880EKFD/",
"accession": "IGVFFI7880EKFD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR3_Rep2_S69"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1267BFAZ/",
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},
{
"@id": "/configuration-files/IGVFFI5950IUVE/",
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},
{
"@id": "/configuration-files/IGVFFI0280XBBS/",
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],
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},
{
"@id": "/configuration-files/IGVFFI7382XUPK/",
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],
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"href": "/configuration-files/IGVFFI7382XUPK/@@download/IGVFFI7382XUPK.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1890CWFB/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6222XYKL/",
"accession": "IGVFFI6222XYKL",
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],
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"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5560HMQA/",
"accession": "IGVFDS5560HMQA",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep1_S2",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep2_S57",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep1_S8",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep2_S63",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR3_Rep1_S14",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR3_Rep2_S69",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR4_Rep1_S20",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR4_Rep2_S75"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:19:21.541767+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3954RGXF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3954RGXF",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep1_S2",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR1_Rep2_S57",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep1_S8",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR2_Rep2_S63",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR3_Rep1_S14",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR3_Rep2_S69",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR4_Rep1_S20",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinB-PCR4_Rep2_S75"
],
"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 B for 10-20% 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": "2024-06-01T01:58:04.312138+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "156deefa-faaf-4730-8478-43866c648284"
}