{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_CS1"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8929VNCP](/auxiliary-sets/IGVFDS8929VNCP/) has sequence file(s): [IGVFFI6893EPCL](/sequence-files/IGVFFI6893EPCL/), [IGVFFI0355AKWQ](/sequence-files/IGVFFI0355AKWQ/), [IGVFFI7148JTBN](/sequence-files/IGVFFI7148JTBN/), [IGVFFI5295OHTL](/sequence-files/IGVFFI5295OHTL/), [IGVFFI3658HZBE](/sequence-files/IGVFFI3658HZBE/), [IGVFFI0332PBFZ](/sequence-files/IGVFFI0332PBFZ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS8929VNCP/"
}
]
},
"award": {
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"component": "functional characterization",
"contact_pi": {
"@id": "/users/eb543cda-67b7-493c-84eb-187d0dac13ba/",
"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"control_for": [],
"creation_timestamp": "2023-12-08T23:52:02.733833+00:00",
"donors": [
{
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"accession": "IGVFDO9208RPQQ",
"aliases": [
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],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
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],
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"creation_timestamp": "2023-12-09T00:50:04.406166+00:00",
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"status": "released",
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"upload_status": "validated"
},
{
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],
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"creation_timestamp": "2023-12-09T00:50:05.892301+00:00",
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"href": "/sequence-files/IGVFFI0355AKWQ/@@download/IGVFFI0355AKWQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/c51f807c-7013-4536-a4bf-89263148e908/IGVFFI0355AKWQ.fastq.gz",
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},
{
"@id": "/sequence-files/IGVFFI7148JTBN/",
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],
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"creation_timestamp": "2023-12-09T00:50:08.356288+00:00",
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"href": "/sequence-files/IGVFFI7148JTBN/@@download/IGVFFI7148JTBN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/9c511f18-90b5-47e6-bb95-0ade66dd670d/IGVFFI7148JTBN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5295OHTL/",
"accession": "IGVFFI5295OHTL",
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],
"content_type": "reads",
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"creation_timestamp": "2023-12-09T00:50:01.911165+00:00",
"file_format": "fastq",
"file_size": 285795540,
"href": "/sequence-files/IGVFFI5295OHTL/@@download/IGVFFI5295OHTL.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3658HZBE/",
"accession": "IGVFFI3658HZBE",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane2_seqlane1_R1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-09T00:50:02.987891+00:00",
"file_format": "fastq",
"file_size": 892252479,
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"s3_uri": "s3://igvf-files/2023/12/09/f6ba8f4f-3549-4cce-867b-5ac7f1500340/IGVFFI3658HZBE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0332PBFZ/",
"accession": "IGVFFI0332PBFZ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane2_seqlane2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:07.151971+00:00",
"file_format": "fastq",
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}
],
"input_for": [
"/analysis-sets/IGVFDS9078ZWQH/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8535CXVX/",
"accession": "IGVFDS8535CXVX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_exprs"
],
"preferred_assay_title": "scCRISPR screen",
"status": "released"
}
],
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1101/2023.03.28.534017",
"doi:10.1038/s41467-024-52490-4"
],
"status": "released"
}
],
"release_timestamp": "2024-08-13T20:47:07.766315+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9390JSDH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9390JSDH",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane2"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7581DNXF/"
],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation",
"status": "released"
}
],
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{
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"@type": [
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"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "K562 cell line (cellular sub pool: 10Xlane2), female, Homo sapiens modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:50:01.911165+00:00",
"summary": "gRNA sequencing for scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "221867df-7fce-4848-bca9-314e60e2d26c"
}