{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_CS1"
],
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"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4502LQQH](/auxiliary-sets/IGVFDS4502LQQH/) has sequence file(s): [IGVFFI9764UXRA](/sequence-files/IGVFFI9764UXRA/), [IGVFFI7570AUYM](/sequence-files/IGVFFI7570AUYM/), [IGVFFI3927QEMS](/sequence-files/IGVFFI3927QEMS/), [IGVFFI4648IIPG](/sequence-files/IGVFFI4648IIPG/), [IGVFFI3189OKPU](/sequence-files/IGVFFI3189OKPU/), [IGVFFI1733REWQ](/sequence-files/IGVFFI1733REWQ/) 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/IGVFDS4502LQQH/"
}
]
},
"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": "2023-12-08T23:52:01.587735+00:00",
"donors": [
{
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"aliases": [
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],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
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"creation_timestamp": "2023-12-09T00:49:55.134660+00:00",
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"status": "released",
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"upload_status": "validated"
},
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},
{
"@id": "/sequence-files/IGVFFI3927QEMS/",
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],
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"creation_timestamp": "2023-12-09T00:49:59.373909+00:00",
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"href": "/sequence-files/IGVFFI3927QEMS/@@download/IGVFFI3927QEMS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/1c2a0d2e-19bb-491e-b43f-4b255c740c10/IGVFFI3927QEMS.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/VP64_CS1_1/VP64_CS1_1_S5_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4648IIPG/",
"accession": "IGVFFI4648IIPG",
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:49:56.417238+00:00",
"file_format": "fastq",
"file_size": 1400676082,
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"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3189OKPU/",
"accession": "IGVFFI3189OKPU",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane1_seqlane1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:49:53.541322+00:00",
"file_format": "fastq",
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"s3_uri": "s3://igvf-files/2023/12/09/2e64dc30-2b54-40ca-aa1c-ef7c46a7312f/IGVFFI3189OKPU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1733REWQ/",
"accession": "IGVFFI1733REWQ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane1_seqlane2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:00.641697+00:00",
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"file_size": 1343287746,
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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/VP64_CS1_1/VP64_CS1_1_S5_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9078ZWQH/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4863BMGZ/",
"accession": "IGVFDS4863BMGZ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_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": "2024-08-13T20:47:08.255390+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4521QSSO/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4521QSSO",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane1"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7581DNXF/"
],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
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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, 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": "2023-12-09T00:49:53.541322+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": "0dc9ea2d-ca73-4152-ba67-3f2d3aedad75"
}