{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8794YVNF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8794YVNF",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep1_S6",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep2_S61",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
"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 [IGVFDS8794YVNF](/auxiliary-sets/IGVFDS8794YVNF/) has sequence file(s) [IGVFFI2406URSZ](/sequence-files/IGVFFI2406URSZ/), [IGVFFI8406TKIY](/sequence-files/IGVFFI8406TKIY/), [IGVFFI1943WFER](/sequence-files/IGVFFI1943WFER/), [IGVFFI3544BRUD](/sequence-files/IGVFFI3544BRUD/), [IGVFFI2688NUHF](/sequence-files/IGVFFI2688NUHF/), [IGVFFI9742FWEW](/sequence-files/IGVFFI9742FWEW/), [IGVFFI2723OPXS](/sequence-files/IGVFFI2723OPXS/), [IGVFFI2265SRGR](/sequence-files/IGVFFI2265SRGR/) 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/IGVFDS8794YVNF/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8794YVNF](/auxiliary-sets/IGVFDS8794YVNF/) 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/IGVFDS8794YVNF/"
}
]
},
"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": "2024-05-21T17:12:28.022055+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/IGVFFI2406URSZ/",
"accession": "IGVFFI2406URSZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep1_S6"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:17.438390+00:00",
"file_format": "fastq",
"file_size": 37381415,
"href": "/sequence-files/IGVFFI2406URSZ/@@download/IGVFFI2406URSZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b7036fa4-6143-4a60-a9f9-5efd18922389/IGVFFI2406URSZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinF-PCR1-Rep1_S6_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6594CJQE/",
"accession": "IGVFFI6594CJQE",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep1_S6"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:44.948022+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI6594CJQE/@@download/IGVFFI6594CJQE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8d976e95-1292-47ff-b157-c6b6c75674e1/IGVFFI6594CJQE.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinF-PCR1_Rep1_S6.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8406TKIY/",
"accession": "IGVFFI8406TKIY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:56.909628+00:00",
"file_format": "fastq",
"file_size": 31933894,
"href": "/sequence-files/IGVFFI8406TKIY/@@download/IGVFFI8406TKIY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/413f6cdc-392c-471c-ac7d-8e1f24a761e3/IGVFFI8406TKIY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinF-PCR2-Rep1_S12_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8822UQNI/",
"accession": "IGVFFI8822UQNI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:40.425295+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI8822UQNI/@@download/IGVFFI8822UQNI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/36e0bcdb-1937-4352-b267-ddf6b8fefc1c/IGVFFI8822UQNI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9867ZSRT/",
"accession": "IGVFFI9867ZSRT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:08.487635+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI9867ZSRT/@@download/IGVFFI9867ZSRT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/54e48b52-8b8b-4a4c-84dc-6b2f2948ed71/IGVFFI9867ZSRT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1943WFER/",
"accession": "IGVFFI1943WFER",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep2_S61"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:37.660452+00:00",
"file_format": "fastq",
"file_size": 19794181,
"href": "/sequence-files/IGVFFI1943WFER/@@download/IGVFFI1943WFER.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/82b14c2f-9564-4d5d-b873-529d7e381aa3/IGVFFI1943WFER.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinF-PCR1-Rep2_S61_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3544BRUD/",
"accession": "IGVFFI3544BRUD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:41.130596+00:00",
"file_format": "fastq",
"file_size": 24665296,
"href": "/sequence-files/IGVFFI3544BRUD/@@download/IGVFFI3544BRUD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3b7f6bc4-6669-4bac-8f1a-522dcf38acdd/IGVFFI3544BRUD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinF-PCR4-Rep2_S79_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2688NUHF/",
"accession": "IGVFFI2688NUHF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:19.166385+00:00",
"file_format": "fastq",
"file_size": 40212238,
"href": "/sequence-files/IGVFFI2688NUHF/@@download/IGVFFI2688NUHF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ee9c3087-1e62-4bc6-b67a-748f71ac2b7b/IGVFFI2688NUHF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinF-PCR2-Rep2_S67_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9742FWEW/",
"accession": "IGVFFI9742FWEW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:38.514940+00:00",
"file_format": "fastq",
"file_size": 36457133,
"href": "/sequence-files/IGVFFI9742FWEW/@@download/IGVFFI9742FWEW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e9f621b2-b5c9-4a0c-a42c-709ba9d1d4f7/IGVFFI9742FWEW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinF-PCR3-Rep1_S18_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2723OPXS/",
"accession": "IGVFFI2723OPXS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:59.645365+00:00",
"file_format": "fastq",
"file_size": 12783282,
"href": "/sequence-files/IGVFFI2723OPXS/@@download/IGVFFI2723OPXS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6d065362-0aa7-4cfb-be66-b9cc60c68496/IGVFFI2723OPXS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinF-PCR3-Rep2_S73_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2265SRGR/",
"accession": "IGVFFI2265SRGR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:20.266113+00:00",
"file_format": "fastq",
"file_size": 42408402,
"href": "/sequence-files/IGVFFI2265SRGR/@@download/IGVFFI2265SRGR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/520ece69-a05f-4369-b4f1-0b8fffb2fbb8/IGVFFI2265SRGR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1926CUXK/",
"accession": "IGVFFI1926CUXK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:26.043776+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1926CUXK/@@download/IGVFFI1926CUXK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4d06d723-41b8-442b-9cbc-2d10b702c072/IGVFFI1926CUXK.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6830TVJW/",
"accession": "IGVFFI6830TVJW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep2_S61"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:58.463411+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI6830TVJW/@@download/IGVFFI6830TVJW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0fb7438a-ed37-4a14-a975-657d179265df/IGVFFI6830TVJW.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3988VDKG/",
"accession": "IGVFFI3988VDKG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:12.056582+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI3988VDKG/@@download/IGVFFI3988VDKG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/71f7dffc-0fa4-4811-9d7e-ae7ea00b2959/IGVFFI3988VDKG.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6628HKXW/",
"accession": "IGVFFI6628HKXW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:54.437357+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI6628HKXW/@@download/IGVFFI6628HKXW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/341b8a48-cbeb-460d-af60-346ba36009b7/IGVFFI6628HKXW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0668QZUU/",
"accession": "IGVFFI0668QZUU",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:22.549624+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI0668QZUU/@@download/IGVFFI0668QZUU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a1d270f4-657c-48d5-97fc-2b8099d838b7/IGVFFI0668QZUU.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1500HTAU/",
"accession": "IGVFDS1500HTAU",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep1_S6",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep2_S61",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:19:50.713446+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5744WHTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5744WHTT",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep1_S6",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR1_Rep2_S61",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep1_S12",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR2_Rep2_S67",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep1_S18",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR3_Rep2_S73",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep1_S24",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinF-PCR4_Rep2_S79"
],
"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 F for 80-100% 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": "2024-06-01T01:58:17.438390+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c5028f1b-d093-4f7c-bd89-b53a2fb108aa"
}