{
"@context": "/terms/",
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"FileSet",
"Item"
],
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],
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"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
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"NOT_COMPLIANT": [
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4863BMGZ](/measurement-sets/IGVFDS4863BMGZ/) has a sequence file [IGVFFI5106LXXU](/sequence-files/IGVFFI5106LXXU/) missing `read_names`. Sequence files are expected to have read names.",
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"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4863BMGZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4863BMGZ](/measurement-sets/IGVFDS4863BMGZ/) has a sequence file [IGVFFI6599UWGY](/sequence-files/IGVFFI6599UWGY/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4863BMGZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4863BMGZ](/measurement-sets/IGVFDS4863BMGZ/) has a sequence file [IGVFFI3105RHFR](/sequence-files/IGVFFI3105RHFR/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4863BMGZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4863BMGZ](/measurement-sets/IGVFDS4863BMGZ/) has a sequence file [IGVFFI8326SURF](/sequence-files/IGVFFI8326SURF/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4863BMGZ/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS4863BMGZ](/measurement-sets/IGVFDS4863BMGZ/) has an `assay_term` of in vitro CRISPR screen using single-cell RNA-seq but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS4863BMGZ/"
}
]
},
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],
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"status": "released"
}
],
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"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
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{
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"summary": "GRCh38 guide RNA sequences"
}
],
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}
],
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"creation_timestamp": "2023-12-08T23:53:36.807086+00:00",
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],
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{
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],
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"status": "released",
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}
],
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"file_set_type": "experimental data",
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},
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"upload_status": "validated"
},
{
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},
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"upload_status": "validated"
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{
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},
{
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"creation_timestamp": "2025-04-15T22:46:53.707247+00:00",
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"status": "in progress",
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}
],
"input_for": [
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],
"lab": {
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"title": "Jay Shendure, UW"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set. This measurement set previously did not specify a preferred_assay_title, but the property is now required so it has been defaulted to SUPERSTARR. Please update with an appropriate preferred_assay_title. This measurement set previously used 5' to 3' as strand_specificity, but the strand_specificity has now been updated to 5 prime to 3 prime via an upgrade.",
"preferred_assay_title": "scCRISPR screen",
"protocols": [
"https://www.protocols.io/view/methods-from-multiplex-single-cell-crispra-screeni-c5zvy766"
],
"publications": [
{
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"publication_identifiers": [
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],
"status": "released"
}
],
"release_timestamp": "2024-08-13T20:47:07.511463+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4521QSSO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4521QSSO",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane1"
],
"cellular_sub_pool": "10Xlane1",
"classifications": [
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],
"institutional_certificates": [],
"modifications": [
{
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"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane1) modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"strand_specificity": "5 prime to 3 prime",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:49:53.541322+00:00",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "4b1872ed-da59-488b-ad5c-b5ff2a763a76"
}