{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2805FQAD/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2805FQAD",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep2_S56",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep1_S7",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep1_S13",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep1_S19",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep2_S74"
],
"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 [IGVFDS2805FQAD](/auxiliary-sets/IGVFDS2805FQAD/) has sequence file(s) [IGVFFI8310ZXDQ](/sequence-files/IGVFFI8310ZXDQ/), [IGVFFI9473RAYZ](/sequence-files/IGVFFI9473RAYZ/), [IGVFFI7962MDES](/sequence-files/IGVFFI7962MDES/), [IGVFFI1423QMWB](/sequence-files/IGVFFI1423QMWB/), [IGVFFI7230YSEB](/sequence-files/IGVFFI7230YSEB/), [IGVFFI5243KTWV](/sequence-files/IGVFFI5243KTWV/), [IGVFFI8079GYLE](/sequence-files/IGVFFI8079GYLE/), [IGVFFI5803HMJL](/sequence-files/IGVFFI5803HMJL/) 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/IGVFDS2805FQAD/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS2805FQAD](/auxiliary-sets/IGVFDS2805FQAD/) 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/IGVFDS2805FQAD/"
}
]
},
"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": "2024-05-21T17:12:21.856032+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": "IGVFFI8310ZXDQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1"
],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 25848089,
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"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5214MZXB/",
"accession": "IGVFFI5214MZXB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:45:33.838309+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5214MZXB/@@download/IGVFFI5214MZXB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/151aa6d4-45df-4173-b5a8-b8268394b71a/IGVFFI5214MZXB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9473RAYZ/",
"accession": "IGVFFI9473RAYZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:59:42.089432+00:00",
"file_format": "fastq",
"file_size": 22662868,
"href": "/sequence-files/IGVFFI9473RAYZ/@@download/IGVFFI9473RAYZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/60d1cb10-f76d-427b-b42a-1af6c356d185/IGVFFI9473RAYZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinA-PCR3-Rep2_S68_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7962MDES/",
"accession": "IGVFFI7962MDES",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep1_S19"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:03.579040+00:00",
"file_format": "fastq",
"file_size": 45207370,
"href": "/sequence-files/IGVFFI7962MDES/@@download/IGVFFI7962MDES.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9cb0fd0e-2e8b-41e0-960f-09f006e6eb88/IGVFFI7962MDES.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinA-PCR4-Rep1_S19_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1187NSVW/",
"accession": "IGVFFI1187NSVW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:46:14.221290+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI1187NSVW/@@download/IGVFFI1187NSVW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7196e980-e878-40cc-9892-7b3b346eef2a/IGVFFI1187NSVW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1423QMWB/",
"accession": "IGVFFI1423QMWB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep2_S56"
],
"content_type": "reads",
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"href": "/sequence-files/IGVFFI1423QMWB/@@download/IGVFFI1423QMWB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5530b846-0b58-4518-859c-e857638208bd/IGVFFI1423QMWB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinA-PCR1-Rep2_S56_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7230YSEB/",
"accession": "IGVFFI7230YSEB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep1_S7"
],
"content_type": "reads",
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"file_format": "fastq",
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"href": "/sequence-files/IGVFFI7230YSEB/@@download/IGVFFI7230YSEB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7b5463fd-246f-424a-8ff0-7b725fb0ee51/IGVFFI7230YSEB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF1-BinA-PCR2-Rep1_S7_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5243KTWV/",
"accession": "IGVFFI5243KTWV",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62"
],
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"href": "/sequence-files/IGVFFI5243KTWV/@@download/IGVFFI5243KTWV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c7456243-15d3-42ff-9e11-388cff09b67a/IGVFFI5243KTWV.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8079GYLE/",
"accession": "IGVFFI8079GYLE",
"aliases": [
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],
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"s3_uri": "s3://igvf-files/2024/06/01/aebff71d-f03b-4ad2-9100-3cef6c186036/IGVFFI8079GYLE.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7581WSTY/",
"accession": "IGVFFI7581WSTY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68"
],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5803HMJL/",
"accession": "IGVFFI5803HMJL",
"aliases": [
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1828YSPU/",
"accession": "IGVFFI1828YSPU",
"aliases": [
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],
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"href": "/configuration-files/IGVFFI1828YSPU/@@download/IGVFFI1828YSPU.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5e93660b-3fcb-4a87-b50d-cbc29dd645e4/IGVFFI1828YSPU.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9037LWHV/",
"accession": "IGVFFI9037LWHV",
"aliases": [
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],
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"href": "/configuration-files/IGVFFI9037LWHV/@@download/IGVFFI9037LWHV.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7191HPTH/",
"accession": "IGVFFI7191HPTH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep1_S13"
],
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"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI7191HPTH/@@download/IGVFFI7191HPTH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/21ddc3c9-588d-4d25-83e1-9a253017fb63/IGVFFI7191HPTH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinA-PCR3_Rep1_S13.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6056WYCZ/",
"accession": "IGVFFI6056WYCZ",
"aliases": [
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],
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"href": "/configuration-files/IGVFFI6056WYCZ/@@download/IGVFFI6056WYCZ.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5319VYHW/",
"accession": "IGVFFI5319VYHW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep2_S74"
],
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"creation_timestamp": "2024-06-11T20:47:10.778723+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI5319VYHW/@@download/IGVFFI5319VYHW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/6bc39ad3-bfb8-4497-9160-21ac52e7d60d/IGVFFI5319VYHW.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF1-BinA-PCR4_Rep2_S74.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1298BFAZ/",
"accession": "IGVFDS1298BFAZ",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep2_S56",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep1_S7",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep1_S13",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep1_S19",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep2_S74"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:19:14.452384+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3086DQMC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3086DQMC",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep1_S1",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR1_Rep2_S56",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep1_S7",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR2_Rep2_S62",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep1_S13",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR3_Rep2_S68",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep1_S19",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF1-BinA-PCR4_Rep2_S74"
],
"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 A for 0-10% 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": "2024-06-01T01:58:01.097868+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "da116226-ab43-4a55-bd1c-ac9cdf19010c"
}