{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5581ABLR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5581ABLR",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep1_S5",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep2_S60",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep1_S11",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep2_S66",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep1_S17",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep2_S72",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep1_S23",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep2_S78"
],
"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 [IGVFDS5581ABLR](/auxiliary-sets/IGVFDS5581ABLR/) has sequence file(s) [IGVFFI9575IHNR](/sequence-files/IGVFFI9575IHNR/), [IGVFFI7367BUVJ](/sequence-files/IGVFFI7367BUVJ/), [IGVFFI1014ZQSZ](/sequence-files/IGVFFI1014ZQSZ/), [IGVFFI8734SFUZ](/sequence-files/IGVFFI8734SFUZ/), [IGVFFI4836TTVK](/sequence-files/IGVFFI4836TTVK/), [IGVFFI1666IWMV](/sequence-files/IGVFFI1666IWMV/), [IGVFFI0132JLWC](/sequence-files/IGVFFI0132JLWC/), [IGVFFI5386XIKZ](/sequence-files/IGVFFI5386XIKZ/) 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/IGVFDS5581ABLR/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5581ABLR](/auxiliary-sets/IGVFDS5581ABLR/) 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/IGVFDS5581ABLR/"
}
]
},
"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": "2024-05-21T17:12:27.098824+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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{
"@id": "/sequence-files/IGVFFI9575IHNR/",
"accession": "IGVFFI9575IHNR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep1_S5"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:13.987116+00:00",
"file_format": "fastq",
"file_size": 40093695,
"href": "/sequence-files/IGVFFI9575IHNR/@@download/IGVFFI9575IHNR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/56db3e98-9cab-4d30-bc1e-ae4890067edd/IGVFFI9575IHNR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9621PMLC/",
"accession": "IGVFFI9621PMLC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep1_S5"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:42.667592+00:00",
"file_format": "yaml",
"file_size": 909,
"href": "/configuration-files/IGVFFI9621PMLC/@@download/IGVFFI9621PMLC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d8da8d8d-c71a-429e-a9fd-9215b4d6a79c/IGVFFI9621PMLC.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinE-PCR1_Rep1_S5.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6531PQSC/",
"accession": "IGVFFI6531PQSC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep2_S72"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:52.197874+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI6531PQSC/@@download/IGVFFI6531PQSC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/49efd175-c0cc-4a9c-94c1-b2cecd6b5ca4/IGVFFI6531PQSC.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinE-PCR3_Rep2_S72.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7367BUVJ/",
"accession": "IGVFFI7367BUVJ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep2_S78"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:38.029527+00:00",
"file_format": "fastq",
"file_size": 14397491,
"href": "/sequence-files/IGVFFI7367BUVJ/@@download/IGVFFI7367BUVJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/0cfec858-4b69-4609-8cbd-d95ad3a79700/IGVFFI7367BUVJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinE-PCR4-Rep2_S78_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1014ZQSZ/",
"accession": "IGVFFI1014ZQSZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep1_S17"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:35.193009+00:00",
"file_format": "fastq",
"file_size": 37716313,
"href": "/sequence-files/IGVFFI1014ZQSZ/@@download/IGVFFI1014ZQSZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e3f92caa-efe1-4bf6-ad47-346aab2da110/IGVFFI1014ZQSZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinE-PCR3-Rep1_S17_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8734SFUZ/",
"accession": "IGVFFI8734SFUZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep2_S60"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:33.920447+00:00",
"file_format": "fastq",
"file_size": 30771841,
"href": "/sequence-files/IGVFFI8734SFUZ/@@download/IGVFFI8734SFUZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/71877db6-8132-4287-ae14-bbb99854f4a9/IGVFFI8734SFUZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinE-PCR1-Rep2_S60_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4836TTVK/",
"accession": "IGVFFI4836TTVK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep1_S11"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:58:53.696651+00:00",
"file_format": "fastq",
"file_size": 29876738,
"href": "/sequence-files/IGVFFI4836TTVK/@@download/IGVFFI4836TTVK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/f68d876d-7bfb-4cd7-bf1c-7e18bd4cb5cd/IGVFFI4836TTVK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1666IWMV/",
"accession": "IGVFFI1666IWMV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep2_S66"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:16.088409+00:00",
"file_format": "fastq",
"file_size": 28817078,
"href": "/sequence-files/IGVFFI1666IWMV/@@download/IGVFFI1666IWMV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/417df1e0-bd57-4bbc-a52d-15c59c1d2e62/IGVFFI1666IWMV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0132JLWC/",
"accession": "IGVFFI0132JLWC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep2_S72"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:56.625450+00:00",
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"file_size": 10138681,
"href": "/sequence-files/IGVFFI0132JLWC/@@download/IGVFFI0132JLWC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b0ee5a12-4c4b-4db1-9bd2-50e65860649f/IGVFFI0132JLWC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinE-PCR3-Rep2_S72_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5386XIKZ/",
"accession": "IGVFFI5386XIKZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep1_S23"
],
"content_type": "reads",
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"file_size": 49369188,
"href": "/sequence-files/IGVFFI5386XIKZ/@@download/IGVFFI5386XIKZ.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9587XVMG/",
"accession": "IGVFFI9587XVMG",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep1_S11"
],
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"href": "/configuration-files/IGVFFI9587XVMG/@@download/IGVFFI9587XVMG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9b4b2f64-ca23-412e-867d-28dfd7de78f0/IGVFFI9587XVMG.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5630OODH/",
"accession": "IGVFFI5630OODH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep2_S66"
],
"content_type": "seqspec",
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"href": "/configuration-files/IGVFFI5630OODH/@@download/IGVFFI5630OODH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/87fce8ab-25d3-4859-a2fb-62431394455d/IGVFFI5630OODH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinE-PCR2_Rep2_S66.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9278SIJZ/",
"accession": "IGVFFI9278SIJZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep2_S60"
],
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"href": "/configuration-files/IGVFFI9278SIJZ/@@download/IGVFFI9278SIJZ.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8014JOBB/",
"accession": "IGVFFI8014JOBB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep1_S17"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:38.076549+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI8014JOBB/@@download/IGVFFI8014JOBB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2c2944f1-a04e-4ca1-a1b4-078f255e59f3/IGVFFI8014JOBB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinE-PCR3_Rep1_S17.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6337ALBZ/",
"accession": "IGVFFI6337ALBZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep1_S23"
],
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"href": "/configuration-files/IGVFFI6337ALBZ/@@download/IGVFFI6337ALBZ.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3637ZSNH/",
"accession": "IGVFFI3637ZSNH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep2_S78"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:20.223027+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI3637ZSNH/@@download/IGVFFI3637ZSNH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8e3e5833-280a-4ed0-aad5-a36dc2e119bf/IGVFFI3637ZSNH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinE-PCR4_Rep2_S78.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6323AUPJ/",
"accession": "IGVFDS6323AUPJ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep1_S5",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep2_S60",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep1_S11",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep2_S66",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep1_S17",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep2_S72",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep1_S23",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep2_S78"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:19:44.130145+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7084WNRY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7084WNRY",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep1_S5",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR1_Rep2_S60",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep1_S11",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR2_Rep2_S66",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep1_S17",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR3_Rep2_S72",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep1_S23",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinE-PCR4_Rep2_S78"
],
"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 E for 80-90% 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": "2024-06-01T01:58:13.987116+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "83cb3e5f-a4fa-457d-b228-2739486a78ab"
}