{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6296UIVP/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6296UIVP",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep1_S30",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep2_S85",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep1_S36",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep1_S42",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep2_S97",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103"
],
"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 [IGVFDS6296UIVP](/auxiliary-sets/IGVFDS6296UIVP/) has sequence file(s) [IGVFFI6708LGQK](/sequence-files/IGVFFI6708LGQK/), [IGVFFI8897HGJW](/sequence-files/IGVFFI8897HGJW/), [IGVFFI0849URVD](/sequence-files/IGVFFI0849URVD/), [IGVFFI4236ZKZQ](/sequence-files/IGVFFI4236ZKZQ/), [IGVFFI4472ZCED](/sequence-files/IGVFFI4472ZCED/), [IGVFFI5078FJXF](/sequence-files/IGVFFI5078FJXF/), [IGVFFI8775RJJR](/sequence-files/IGVFFI8775RJJR/), [IGVFFI8620KXPV](/sequence-files/IGVFFI8620KXPV/) 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/IGVFDS6296UIVP/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6296UIVP](/auxiliary-sets/IGVFDS6296UIVP/) 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/IGVFDS6296UIVP/"
}
]
},
"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": "2024-05-21T17:13:10.419044+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": "IGVFFI6708LGQK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep1_S30"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:02.263131+00:00",
"file_format": "fastq",
"file_size": 46995707,
"href": "/sequence-files/IGVFFI6708LGQK/@@download/IGVFFI6708LGQK.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4839KCLK/",
"accession": "IGVFFI4839KCLK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep1_S30"
],
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"creation_timestamp": "2024-06-11T20:47:37.291173+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI4839KCLK/@@download/IGVFFI4839KCLK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/87eaa7ef-10fa-4fe3-8eb0-81e5d4e7381b/IGVFFI4839KCLK.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1820NGCT/",
"accession": "IGVFFI1820NGCT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:48:20.044242+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1820NGCT/@@download/IGVFFI1820NGCT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/478b68eb-ae82-44d8-baae-f58bc022840f/IGVFFI1820NGCT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5346CYNH/",
"accession": "IGVFFI5346CYNH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48"
],
"content_type": "seqspec",
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"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5346CYNH/@@download/IGVFFI5346CYNH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/60b1ac54-ffac-479d-8f00-40bd63bc273d/IGVFFI5346CYNH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8897HGJW/",
"accession": "IGVFFI8897HGJW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep2_S85"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:22.445162+00:00",
"file_format": "fastq",
"file_size": 13657852,
"href": "/sequence-files/IGVFFI8897HGJW/@@download/IGVFFI8897HGJW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/80e40c1a-568f-4ad7-8451-286356751151/IGVFFI8897HGJW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinF-PCR1-Rep2_S85_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0849URVD/",
"accession": "IGVFFI0849URVD",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep1_S36"
],
"content_type": "reads",
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"href": "/sequence-files/IGVFFI0849URVD/@@download/IGVFFI0849URVD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b2a10f0b-3dc8-48a3-afa4-53cb44cdb37f/IGVFFI0849URVD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4236ZKZQ/",
"accession": "IGVFFI4236ZKZQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91"
],
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"href": "/sequence-files/IGVFFI4236ZKZQ/@@download/IGVFFI4236ZKZQ.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4472ZCED/",
"accession": "IGVFFI4472ZCED",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48"
],
"content_type": "reads",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5078FJXF/",
"accession": "IGVFFI5078FJXF",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8775RJJR/",
"accession": "IGVFFI8775RJJR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep1_S42"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8620KXPV/",
"accession": "IGVFFI8620KXPV",
"aliases": [
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7674FVAU/",
"accession": "IGVFFI7674FVAU",
"aliases": [
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],
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"href": "/configuration-files/IGVFFI7674FVAU/@@download/IGVFFI7674FVAU.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6042PRCO/",
"accession": "IGVFFI6042PRCO",
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],
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"href": "/configuration-files/IGVFFI6042PRCO/@@download/IGVFFI6042PRCO.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1174FSAA/",
"accession": "IGVFFI1174FSAA",
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"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep1_S36"
],
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"href": "/configuration-files/IGVFFI1174FSAA/@@download/IGVFFI1174FSAA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/3eb23655-9bc4-4380-8c94-8fdb859cb85e/IGVFFI1174FSAA.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3084HVWV/",
"accession": "IGVFFI3084HVWV",
"aliases": [
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5121TSVZ/",
"accession": "IGVFFI5121TSVZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103"
],
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"href": "/configuration-files/IGVFFI5121TSVZ/@@download/IGVFFI5121TSVZ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/fcc7a8c2-ea9c-4df4-a85c-4cbd37b32c41/IGVFFI5121TSVZ.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6224TNVO/",
"accession": "IGVFDS6224TNVO",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep1_S30",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep2_S85",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep1_S36",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep1_S42",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep2_S97",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:20:38.875417+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9724UBWS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9724UBWS",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep1_S30",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR1_Rep2_S85",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep1_S36",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR2_Rep2_S91",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep1_S42",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR3_Rep2_S97",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep1_S48",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinF-PCR4_Rep2_S103"
],
"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": "2024-06-01T02:01:02.263131+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "333c644e-82cd-4b07-9436-0df86ca63d62"
}