{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane2_CS1"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4834SKZS](/auxiliary-sets/IGVFDS4834SKZS/) has sequence file(s): [IGVFFI6797WWMA](/sequence-files/IGVFFI6797WWMA/), [IGVFFI4295KZWO](/sequence-files/IGVFFI4295KZWO/), [IGVFFI3777QEJF](/sequence-files/IGVFFI3777QEJF/), [IGVFFI1773NVFV](/sequence-files/IGVFFI1773NVFV/), [IGVFFI2340WJKO](/sequence-files/IGVFFI2340WJKO/), [IGVFFI2735DIDC](/sequence-files/IGVFFI2735DIDC/) 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/IGVFDS4834SKZS/"
}
]
},
"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": "2023-12-08T23:52:04.774411+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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"creation_timestamp": "2023-12-09T00:50:35.278739+00:00",
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"status": "released",
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},
{
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{
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"creation_timestamp": "2023-12-09T00:50:33.163490+00:00",
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"href": "/sequence-files/IGVFFI3777QEJF/@@download/IGVFFI3777QEJF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/c68d0c8d-3311-4d37-9fd3-0b612a3ba194/IGVFFI3777QEJF.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_2/VPR_CS1_2_S8_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1773NVFV/",
"accession": "IGVFFI1773NVFV",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane2_seqlane2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:36.362660+00:00",
"file_format": "fastq",
"file_size": 302685992,
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"s3_uri": "s3://igvf-files/2023/12/09/ddfe29dd-0f8c-4cfc-a3ff-ee1b28699092/IGVFFI1773NVFV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2340WJKO/",
"accession": "IGVFFI2340WJKO",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane2_seqlane2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:37.493167+00:00",
"file_format": "fastq",
"file_size": 823982023,
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"s3_uri": "s3://igvf-files/2023/12/09/63ba4dad-97bb-4b77-af6f-a4a12f94dce4/IGVFFI2340WJKO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2735DIDC/",
"accession": "IGVFFI2735DIDC",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane2_seqlane1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:34.211741+00:00",
"file_format": "fastq",
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"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_2/VPR_CS1_2_S8_L001_R1_001.fastq.gz",
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}
],
"input_for": [
"/analysis-sets/IGVFDS9078ZWQH/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0508ERUQ/",
"accession": "IGVFDS0508ERUQ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_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": "2024-08-13T20:47:07.970045+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9542NUGS/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9542NUGS",
"aliases": [
"jay-shendure:CRISPRa_VPR_K562_10Xlane2"
],
"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: 10Xlane2), 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": "2023-12-09T00:50:33.163490+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": "20f51543-1cd9-43d7-95f2-f4e50179cab3"
}