{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3139RYUI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3139RYUI",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep2_S88",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep1_S45",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep2_S100"
],
"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 [IGVFDS3139RYUI](/auxiliary-sets/IGVFDS3139RYUI/) has sequence file(s) [IGVFFI1435MZPM](/sequence-files/IGVFFI1435MZPM/), [IGVFFI8754LKYF](/sequence-files/IGVFFI8754LKYF/), [IGVFFI3364QZVW](/sequence-files/IGVFFI3364QZVW/), [IGVFFI4506XCFK](/sequence-files/IGVFFI4506XCFK/), [IGVFFI2767JLED](/sequence-files/IGVFFI2767JLED/), [IGVFFI9428EDUT](/sequence-files/IGVFFI9428EDUT/), [IGVFFI0106GQNO](/sequence-files/IGVFFI0106GQNO/), [IGVFFI8510KORF](/sequence-files/IGVFFI8510KORF/) 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/IGVFDS3139RYUI/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS3139RYUI](/auxiliary-sets/IGVFDS3139RYUI/) 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/IGVFDS3139RYUI/"
}
]
},
"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": "2024-05-21T17:13:08.147683+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/IGVFFI1435MZPM/",
"accession": "IGVFFI1435MZPM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:51.441233+00:00",
"file_format": "fastq",
"file_size": 37174553,
"href": "/sequence-files/IGVFFI1435MZPM/@@download/IGVFFI1435MZPM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/64df2ac5-4402-4734-96c4-f179899a0193/IGVFFI1435MZPM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinC-PCR1-Rep1_S27_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6248PVCU/",
"accession": "IGVFFI6248PVCU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:30.041121+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI6248PVCU/@@download/IGVFFI6248PVCU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/968dd58c-f807-4d91-8078-58acc46dd011/IGVFFI6248PVCU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8754LKYF/",
"accession": "IGVFFI8754LKYF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep2_S100"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:03:20.937047+00:00",
"file_format": "fastq",
"file_size": 21829999,
"href": "/sequence-files/IGVFFI8754LKYF/@@download/IGVFFI8754LKYF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e4d34a50-808c-443c-aecb-1455a11125d7/IGVFFI8754LKYF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinC-PCR4-Rep2_S100_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1879WVBZ/",
"accession": "IGVFFI1879WVBZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:27.475324+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1879WVBZ/@@download/IGVFFI1879WVBZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/25e28cfe-3bfe-4d96-bbfd-1af7cc3ca49e/IGVFFI1879WVBZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3205EXPI/",
"accession": "IGVFFI3205EXPI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:41.751425+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI3205EXPI/@@download/IGVFFI3205EXPI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/05249149-ea1e-47f4-878b-03c8c5f9500b/IGVFFI3205EXPI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3364QZVW/",
"accession": "IGVFFI3364QZVW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep1_S45"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:59.823395+00:00",
"file_format": "fastq",
"file_size": 38560919,
"href": "/sequence-files/IGVFFI3364QZVW/@@download/IGVFFI3364QZVW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f3302660-9aef-4882-9b7c-f57e7a51f121/IGVFFI3364QZVW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinC-PCR4-Rep1_S45_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4506XCFK/",
"accession": "IGVFFI4506XCFK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:12.399420+00:00",
"file_format": "fastq",
"file_size": 14818710,
"href": "/sequence-files/IGVFFI4506XCFK/@@download/IGVFFI4506XCFK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3258c24f-26dd-4a85-be51-c68d20e495f8/IGVFFI4506XCFK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinC-PCR1-Rep2_S82_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2767JLED/",
"accession": "IGVFFI2767JLED",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:18.529474+00:00",
"file_format": "fastq",
"file_size": 40728751,
"href": "/sequence-files/IGVFFI2767JLED/@@download/IGVFFI2767JLED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/de63b1e0-7848-4138-80f3-892c8e98325f/IGVFFI2767JLED.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinC-PCR3-Rep1_S39_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9428EDUT/",
"accession": "IGVFFI9428EDUT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:38.984316+00:00",
"file_format": "fastq",
"file_size": 15160764,
"href": "/sequence-files/IGVFFI9428EDUT/@@download/IGVFFI9428EDUT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9f3a9312-b10a-45bb-96d3-4367cec069d7/IGVFFI9428EDUT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinC-PCR3-Rep2_S94_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1996ZSTC/",
"accession": "IGVFFI1996ZSTC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep2_S88"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:13.027376+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1996ZSTC/@@download/IGVFFI1996ZSTC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1f65c8f5-5aaa-4a61-b0ef-2bf9f61889cd/IGVFFI1996ZSTC.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR2_Rep2_S88.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2817XXHR/",
"accession": "IGVFFI2817XXHR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:44.504795+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI2817XXHR/@@download/IGVFFI2817XXHR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/dceaf465-c28f-4650-b493-b52667a37ec7/IGVFFI2817XXHR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1384QEIW/",
"accession": "IGVFFI1384QEIW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep1_S45"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:56.125338+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI1384QEIW/@@download/IGVFFI1384QEIW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d56636c8-3e6e-40e8-b7d9-4ed40b5fa6c1/IGVFFI1384QEIW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR4_Rep1_S45.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0106GQNO/",
"accession": "IGVFFI0106GQNO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:36.584010+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI0106GQNO/@@download/IGVFFI0106GQNO.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8510KORF/",
"accession": "IGVFFI8510KORF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep2_S88"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:57.700416+00:00",
"file_format": "fastq",
"file_size": 19535767,
"href": "/sequence-files/IGVFFI8510KORF/@@download/IGVFFI8510KORF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/69b7ed15-19b6-44c5-9c48-77f417379d6e/IGVFFI8510KORF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinC-PCR2-Rep2_S88_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2776NKVA/",
"accession": "IGVFFI2776NKVA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33"
],
"content_type": "seqspec",
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI2776NKVA/@@download/IGVFFI2776NKVA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/c9628d26-bf4b-42a3-8f3e-51fb58f9aea1/IGVFFI2776NKVA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5550NXVT/",
"accession": "IGVFFI5550NXVT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep2_S100"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:11.113263+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI5550NXVT/@@download/IGVFFI5550NXVT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8ddfbc70-1e4a-4afe-b6c0-057b0fa75928/IGVFFI5550NXVT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinC-PCR4_Rep2_S100.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2427TBFR/",
"accession": "IGVFDS2427TBFR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep2_S88",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep1_S45",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep2_S100"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:20:14.740736+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7258NLNH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7258NLNH",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep1_S27",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR1_Rep2_S82",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep1_S33",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR2_Rep2_S88",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep1_S39",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR3_Rep2_S94",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep1_S45",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinC-PCR4_Rep2_S100"
],
"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": "2024-06-01T02:00:51.441233+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "edb17e5f-a543-42ca-9e45-87395e478cdc"
}