{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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],
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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.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
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},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7359MSBY](/auxiliary-sets/IGVFDS7359MSBY/) has sequence file(s): [IGVFFI0056ELXT](/sequence-files/IGVFFI0056ELXT/), [IGVFFI5659FYZA](/sequence-files/IGVFFI5659FYZA/), [IGVFFI4464QAQU](/sequence-files/IGVFFI4464QAQU/), [IGVFFI0326UVNH](/sequence-files/IGVFFI0326UVNH/) 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/IGVFDS7359MSBY/"
}
]
},
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"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
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"creation_timestamp": "2024-02-06T19:29:43.483144+00:00",
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{
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],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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],
"content_type": "reads",
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"creation_timestamp": "2024-02-06T21:24:37.048232+00:00",
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"upload_status": "validated"
},
{
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],
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4464QAQU/",
"accession": "IGVFFI4464QAQU",
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"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_2_AGGTAAGG_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:24:25.241154+00:00",
"file_format": "fastq",
"file_size": 377757897,
"href": "/sequence-files/IGVFFI4464QAQU/@@download/IGVFFI4464QAQU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/3a928d7c-e6c0-4c3f-acfa-f412974a9161/IGVFFI4464QAQU.fastq.gz",
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"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0326UVNH/",
"accession": "IGVFFI0326UVNH",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_2_AGGTAAGG_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:24:18.286691+00:00",
"file_format": "fastq",
"file_size": 323941303,
"href": "/sequence-files/IGVFFI0326UVNH/@@download/IGVFFI0326UVNH.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_2_AGGTAAGG_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7943IIWZ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9990NLDH/",
"accession": "IGVFDS9990NLDH",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_2"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3104QEEP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3104QEEP",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_2"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1298TUYG/"
],
"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": "12",
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"submitted_by": {
"@id": "/users/4b2083b4-24c1-41d8-9daa-e79299f00d6e/",
"title": "Ronghao Zhou"
},
"submitted_files_timestamp": "2024-02-06T21:24:18.286691+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "4e3e0acc-cdc8-4560-8b17-956e4d2f34bd"
}