{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane1_CS1"
],
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"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4621HUKP](/auxiliary-sets/IGVFDS4621HUKP/) has sequence file(s): [IGVFFI1163CNBZ](/sequence-files/IGVFFI1163CNBZ/), [IGVFFI3887HQZR](/sequence-files/IGVFFI3887HQZR/), [IGVFFI3175HZHT](/sequence-files/IGVFFI3175HZHT/), [IGVFFI5218FTCG](/sequence-files/IGVFFI5218FTCG/), [IGVFFI7439CGLC](/sequence-files/IGVFFI7439CGLC/), [IGVFFI2138EWHH](/sequence-files/IGVFFI2138EWHH/) 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/IGVFDS4621HUKP/"
}
]
},
"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"
},
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"creation_timestamp": "2023-12-08T23:52:03.799708+00:00",
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{
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"aliases": [
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],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"s3_uri": "s3://igvf-files/2023/12/09/4355b444-271d-43c7-b814-a9bf410311a7/IGVFFI3175HZHT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VPR_CS1_1/VPR_CS1_1_S7_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5218FTCG/",
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"aliases": [
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],
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"creation_timestamp": "2023-12-09T00:50:28.008887+00:00",
"file_format": "fastq",
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"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7439CGLC/",
"accession": "IGVFFI7439CGLC",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane1_seqlane2_I1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-09T00:50:29.103903+00:00",
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},
{
"@id": "/sequence-files/IGVFFI2138EWHH/",
"accession": "IGVFFI2138EWHH",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane1_seqlane2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:32.109863+00:00",
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"status": "released",
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}
],
"input_for": [
"/analysis-sets/IGVFDS9078ZWQH/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7395DPAD/",
"accession": "IGVFDS7395DPAD",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane1_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": "2024-08-13T20:47:07.018575+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1594ZOQH/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1594ZOQH",
"aliases": [
"jay-shendure:CRISPRa_VPR_K562_10Xlane1"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7581DNXF/"
],
"modifications": [
{
"@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"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: 10Xlane1), female, Homo sapiens modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), 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": "2023-12-09T00:50:25.812810+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": "9a2a01ab-50e6-49d4-9f27-e9b6b6710896"
}