{
"@context": "/terms/",
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"FileSet",
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],
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],
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"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
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{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4784DDTU](/auxiliary-sets/IGVFDS4784DDTU/) has sequence file(s): [IGVFFI4092GRZQ](/sequence-files/IGVFFI4092GRZQ/), [IGVFFI1378RGUV](/sequence-files/IGVFFI1378RGUV/), [IGVFFI7575DTDH](/sequence-files/IGVFFI7575DTDH/), [IGVFFI4619DNJG](/sequence-files/IGVFFI4619DNJG/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
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"name": "audit_missing_seqspec",
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},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
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"name": "audit_ntr_term_id",
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},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7600PZYR](/measurement-sets/IGVFDS7600PZYR/) has sequence file(s): [IGVFFI4487DHRU](/sequence-files/IGVFFI4487DHRU/), [IGVFFI9049JPTY](/sequence-files/IGVFFI9049JPTY/), [IGVFFI6125WLFU](/sequence-files/IGVFFI6125WLFU/), [IGVFFI2912EVSN](/sequence-files/IGVFFI2912EVSN/), [IGVFFI2157LCVI](/sequence-files/IGVFFI2157LCVI/), [IGVFFI2426GZJV](/sequence-files/IGVFFI2426GZJV/), [IGVFFI8328SBXI](/sequence-files/IGVFFI8328SBXI/), [IGVFFI7882CEIW](/sequence-files/IGVFFI7882CEIW/), [IGVFFI4775GVGW](/sequence-files/IGVFFI4775GVGW/), [IGVFFI5607YHVQ](/sequence-files/IGVFFI5607YHVQ/), [IGVFFI1492IMBA](/sequence-files/IGVFFI1492IMBA/), [IGVFFI4544QBUW](/sequence-files/IGVFFI4544QBUW/), [IGVFFI8003RIWJ](/sequence-files/IGVFFI8003RIWJ/), [IGVFFI6612DJXQ](/sequence-files/IGVFFI6612DJXQ/), [IGVFFI1024CKHO](/sequence-files/IGVFFI1024CKHO/) 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": "/measurement-sets/IGVFDS7600PZYR/"
}
]
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"submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210616_Broad_fastq/scRNAseq_2kG_2PMDox2_1_c_TGAAGTAC_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7943IIWZ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set.",
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/systematic-perturb-seq-to-discover-endothelial-cel-261ged73yv47/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0862BZMH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0862BZMH",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_1"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS1298TUYG/",
"accession": "IGVFDS1298TUYG",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting genes in many genomic loci"
}
],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "preview",
"summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/05fa0dc9-0e33-427c-9d1f-82393edc4a03/",
"title": "Helen Kang"
},
"submitted_files_timestamp": "2023-12-20T23:46:39.750209+00:00",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "506f4995-5647-411b-8af6-6f196bd52da8"
}