{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6346MBBC/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6346MBBC",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep1_S136",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep1_S142",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep2_S197",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep1_S154",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6346MBBC](/auxiliary-sets/IGVFDS6346MBBC/) has sequence file(s) [IGVFFI6733QFQU](/sequence-files/IGVFFI6733QFQU/), [IGVFFI4330WQPV](/sequence-files/IGVFFI4330WQPV/), [IGVFFI9912MXSK](/sequence-files/IGVFFI9912MXSK/), [IGVFFI0285SRTG](/sequence-files/IGVFFI0285SRTG/), [IGVFFI6507QLNG](/sequence-files/IGVFFI6507QLNG/), [IGVFFI9254WOTL](/sequence-files/IGVFFI9254WOTL/), [IGVFFI2079RGSD](/sequence-files/IGVFFI2079RGSD/), [IGVFFI2014UAIA](/sequence-files/IGVFFI2014UAIA/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS6346MBBC/"
}
]
},
"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": "2024-05-21T17:39:58.110587+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"accession": "IGVFFI6733QFQU",
"aliases": [
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],
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"upload_status": "validated"
},
{
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"aliases": [
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],
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI4885SSST/@@download/IGVFFI4885SSST.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4330WQPV/",
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"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148"
],
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"creation_timestamp": "2024-06-01T02:07:34.852493+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9912MXSK/",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203"
],
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"creation_timestamp": "2024-06-01T02:07:53.630038+00:00",
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"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9412OHLV/",
"accession": "IGVFFI9412OHLV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203"
],
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"creation_timestamp": "2024-06-11T20:52:37.311149+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9412OHLV/@@download/IGVFFI9412OHLV.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/2f91c66e-5f98-443e-84aa-4cbe1418268a/IGVFFI9412OHLV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0285SRTG/",
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"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191"
],
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"creation_timestamp": "2024-06-01T02:06:37.675085+00:00",
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"href": "/sequence-files/IGVFFI0285SRTG/@@download/IGVFFI0285SRTG.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6507QLNG/",
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],
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"creation_timestamp": "2024-06-01T02:06:57.278601+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9254WOTL/",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2079RGSD/",
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2014UAIA/",
"accession": "IGVFFI2014UAIA",
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],
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},
{
"@id": "/configuration-files/IGVFFI4783LAYC/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9426DMVM/",
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],
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},
{
"@id": "/configuration-files/IGVFFI1661FFXY/",
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],
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},
{
"@id": "/configuration-files/IGVFFI3568CAMJ/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8534NOKY/",
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],
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8897VNQR/",
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],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6690WAEP/",
"accession": "IGVFDS6690WAEP",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep1_S136",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep1_S142",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep2_S197",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep1_S154",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:21:39.847404+00:00",
"samples": [
{
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"@type": [
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"Biosample",
"Sample",
"Item"
],
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"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR1_Rep2_S191",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep1_S142",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR2_Rep2_S197",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep1_S148",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR3_Rep2_S203",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep1_S154",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinB-PCR4_Rep2_S209"
],
"classifications": [
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],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
{
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},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
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}
],
"sample_terms": [
{
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"@type": [
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"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 B for 10-20% expression of MYC) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:06:15.587546+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a6ece6e8-60db-4f29-91e2-b13c1e3a6f7f"
}