{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6541EVXL/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6541EVXL",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep1_S28",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep2_S83",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep1_S34",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep2_S89",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep1_S40",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep2_S95",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep1_S46",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep2_S101"
],
"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 [IGVFDS6541EVXL](/auxiliary-sets/IGVFDS6541EVXL/) has sequence file(s) [IGVFFI1007CYRL](/sequence-files/IGVFFI1007CYRL/), [IGVFFI3864GYTT](/sequence-files/IGVFFI3864GYTT/), [IGVFFI0409CMRD](/sequence-files/IGVFFI0409CMRD/), [IGVFFI8915JKET](/sequence-files/IGVFFI8915JKET/), [IGVFFI8115RHRN](/sequence-files/IGVFFI8115RHRN/), [IGVFFI0584UVTC](/sequence-files/IGVFFI0584UVTC/), [IGVFFI2004HRIY](/sequence-files/IGVFFI2004HRIY/), [IGVFFI7539GUVK](/sequence-files/IGVFFI7539GUVK/) 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/IGVFDS6541EVXL/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6541EVXL](/auxiliary-sets/IGVFDS6541EVXL/) 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/IGVFDS6541EVXL/"
}
]
},
"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": "2024-05-21T17:13:08.925189+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": "IGVFFI1007CYRL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep1_S28"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:55.081494+00:00",
"file_format": "fastq",
"file_size": 41815259,
"href": "/sequence-files/IGVFFI1007CYRL/@@download/IGVFFI1007CYRL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e2685784-34bd-4913-b3b8-40f01a62e72b/IGVFFI1007CYRL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0070BEQQ/",
"accession": "IGVFFI0070BEQQ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep1_S28"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:32.322295+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0070BEQQ/@@download/IGVFFI0070BEQQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/33ef73ba-a1b6-4783-bfc0-37b443c0c579/IGVFFI0070BEQQ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinD-PCR1_Rep1_S28.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3864GYTT/",
"accession": "IGVFFI3864GYTT",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep2_S95"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:42.279467+00:00",
"file_format": "fastq",
"file_size": 12266407,
"href": "/sequence-files/IGVFFI3864GYTT/@@download/IGVFFI3864GYTT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6db9cba7-7174-41ee-82d0-d8befbed264d/IGVFFI3864GYTT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinD-PCR3-Rep2_S95_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0409CMRD/",
"accession": "IGVFFI0409CMRD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep2_S89"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:01.017342+00:00",
"file_format": "fastq",
"file_size": 31067533,
"href": "/sequence-files/IGVFFI0409CMRD/@@download/IGVFFI0409CMRD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/2e0db319-a565-4fd4-a9a4-d5c977aa042b/IGVFFI0409CMRD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinD-PCR2-Rep2_S89_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8915JKET/",
"accession": "IGVFFI8915JKET",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep2_S83"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:15.680217+00:00",
"file_format": "fastq",
"file_size": 6613921,
"href": "/sequence-files/IGVFFI8915JKET/@@download/IGVFFI8915JKET.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/208b20a6-1e76-4c17-9628-c2e1b9c30e9d/IGVFFI8915JKET.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinD-PCR1-Rep2_S83_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0667ZMOX/",
"accession": "IGVFFI0667ZMOX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep2_S89"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:15.335856+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI0667ZMOX/@@download/IGVFFI0667ZMOX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/50a57406-fcde-49dc-ac29-73c2a91c661c/IGVFFI0667ZMOX.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinD-PCR2_Rep2_S89.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8115RHRN/",
"accession": "IGVFFI8115RHRN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep1_S34"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:40.324198+00:00",
"file_format": "fastq",
"file_size": 37779253,
"href": "/sequence-files/IGVFFI8115RHRN/@@download/IGVFFI8115RHRN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/bab5440c-2a92-4f6d-9127-de1159c93479/IGVFFI8115RHRN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinD-PCR2-Rep1_S34_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0584UVTC/",
"accession": "IGVFFI0584UVTC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep1_S46"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:03:03.158267+00:00",
"file_format": "fastq",
"file_size": 48674633,
"href": "/sequence-files/IGVFFI0584UVTC/@@download/IGVFFI0584UVTC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/280a7f36-4be0-49f2-aab6-161e80b8c4c7/IGVFFI0584UVTC.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7498HUVR/",
"accession": "IGVFFI7498HUVR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep2_S83"
],
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"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI7498HUVR/@@download/IGVFFI7498HUVR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/1d9f4e3e-f03b-49b5-bee3-397d97ac773c/IGVFFI7498HUVR.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinD-PCR1_Rep2_S83.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2004HRIY/",
"accession": "IGVFFI2004HRIY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep1_S40"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:22.062614+00:00",
"file_format": "fastq",
"file_size": 37229125,
"href": "/sequence-files/IGVFFI2004HRIY/@@download/IGVFFI2004HRIY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/42a83818-8842-41a8-adf7-e890f76c59f0/IGVFFI2004HRIY.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7539GUVK/",
"accession": "IGVFFI7539GUVK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep2_S101"
],
"content_type": "reads",
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"file_format": "fastq",
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"s3_uri": "s3://igvf-files/2024/06/01/dac6d8f8-2433-43bb-8f27-7adc23a1a29d/IGVFFI7539GUVK.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6838XQJU/",
"accession": "IGVFFI6838XQJU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep1_S40"
],
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"creation_timestamp": "2024-06-11T20:48:29.951335+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI6838XQJU/@@download/IGVFFI6838XQJU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0d13974e-7bb8-4c49-845a-7380029d403c/IGVFFI6838XQJU.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8671HDLD/",
"accession": "IGVFFI8671HDLD",
"aliases": [
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],
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"href": "/configuration-files/IGVFFI8671HDLD/@@download/IGVFFI8671HDLD.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0369MZCG/",
"accession": "IGVFFI0369MZCG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep2_S95"
],
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"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI0369MZCG/@@download/IGVFFI0369MZCG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2e892f36-2da9-4f90-ab54-9dca4e85fb6a/IGVFFI0369MZCG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinD-PCR3_Rep2_S95.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2787QCSH/",
"accession": "IGVFFI2787QCSH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep1_S46"
],
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"href": "/configuration-files/IGVFFI2787QCSH/@@download/IGVFFI2787QCSH.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1437HJWT/",
"accession": "IGVFFI1437HJWT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep2_S101"
],
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"creation_timestamp": "2024-06-11T20:49:13.625062+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI1437HJWT/@@download/IGVFFI1437HJWT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/262bfd03-b13a-4de4-aad6-96895f14f6d6/IGVFFI1437HJWT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinD-PCR4_Rep2_S101.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4487XERQ/",
"accession": "IGVFDS4487XERQ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep1_S28",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep2_S83",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep1_S34",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep2_S89",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep1_S40",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep2_S95",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep1_S46",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep2_S101"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:20:22.959808+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9894YYOA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9894YYOA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep1_S28",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR1_Rep2_S83",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep1_S34",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR2_Rep2_S89",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep1_S40",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR3_Rep2_S95",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep1_S46",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinD-PCR4_Rep2_S101"
],
"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 D for 55-65% 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": "2024-06-01T02:00:55.081494+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ba77dfea-ddf0-457b-921b-c64a8af04fa6"
}