{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_4"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4800QEKC](/auxiliary-sets/IGVFDS4800QEKC/) has sequence file(s): [IGVFFI3409KWDR](/sequence-files/IGVFFI3409KWDR/), [IGVFFI2858EWEU](/sequence-files/IGVFFI2858EWEU/), [IGVFFI6713EUUQ](/sequence-files/IGVFFI6713EUUQ/), [IGVFFI3141FJJJ](/sequence-files/IGVFFI3141FJJJ/) 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/IGVFDS4800QEKC/"
},
{
"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",
"path": "/sample-terms/NTR_0000753/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
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"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-02-06T19:29:33.183545+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
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],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
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{
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"accession": "IGVFFI3409KWDR",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:19:08.675961+00:00",
"file_format": "fastq",
"file_size": 410815921,
"href": "/sequence-files/IGVFFI3409KWDR/@@download/IGVFFI3409KWDR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/b450fb5c-4135-4b2e-89ef-2833e7c8a5b0/IGVFFI3409KWDR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2858EWEU/",
"accession": "IGVFFI2858EWEU",
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],
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"creation_timestamp": "2024-02-06T21:18:58.820957+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI2858EWEU/@@download/IGVFFI2858EWEU.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6713EUUQ/",
"accession": "IGVFFI6713EUUQ",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_4.2_ATTACTCG_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:19:20.202647+00:00",
"file_format": "fastq",
"file_size": 290603455,
"href": "/sequence-files/IGVFFI6713EUUQ/@@download/IGVFFI6713EUUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/68e46caf-6615-458a-b3f6-aa1473c0b99c/IGVFFI6713EUUQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_11AMDox_4.2_ATTACTCG_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3141FJJJ/",
"accession": "IGVFFI3141FJJJ",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_4.2_ATTACTCG_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:19:14.964311+00:00",
"file_format": "fastq",
"file_size": 292689780,
"href": "/sequence-files/IGVFFI3141FJJJ/@@download/IGVFFI3141FJJJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/094834b3-6c8d-47de-874d-43f9eaefe697/IGVFFI3141FJJJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_11AMDox_4.2_ATTACTCG_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/IGVFDS9186LBQJ/",
"accession": "IGVFDS9186LBQJ",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_4"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6969BXDT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6969BXDT",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_11AMDox_4"
],
"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",
"status": "preview",
"submitted_by": {
"@id": "/users/4b2083b4-24c1-41d8-9daa-e79299f00d6e/",
"title": "Ronghao Zhou"
},
"submitted_files_timestamp": "2024-02-06T21:18:58.820957+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "714587a8-91a9-42dc-86c6-b1ec93c2b191"
}