{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2031LFEN/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2031LFEN",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_6"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2031LFEN](/auxiliary-sets/IGVFDS2031LFEN/) has sequence file(s): [IGVFFI8535CSXL](/sequence-files/IGVFFI8535CSXL/), [IGVFFI4014XSAK](/sequence-files/IGVFFI4014XSAK/), [IGVFFI3955WSPN](/sequence-files/IGVFFI3955WSPN/), [IGVFFI6132PXBN](/sequence-files/IGVFFI6132PXBN/), [IGVFFI5712MZTB](/sequence-files/IGVFFI5712MZTB/), [IGVFFI6559SZAD](/sequence-files/IGVFFI6559SZAD/), [IGVFFI8066GKDM](/sequence-files/IGVFFI8066GKDM/), [IGVFFI0864MICP](/sequence-files/IGVFFI0864MICP/) 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/IGVFDS2031LFEN/"
},
{
"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": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-02-06T19:29:40.654164+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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{
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:22:19.616193+00:00",
"file_format": "fastq",
"file_size": 204030103,
"href": "/sequence-files/IGVFFI8535CSXL/@@download/IGVFFI8535CSXL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/b0a3ad55-8f9b-4f08-9823-91e4c0d50eca/IGVFFI8535CSXL.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_2PMDox1_6_redo_TCCTTGGT_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4014XSAK/",
"accession": "IGVFFI4014XSAK",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_6_redo_TCCTTGGT_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:22:24.233336+00:00",
"file_format": "fastq",
"file_size": 235385801,
"href": "/sequence-files/IGVFFI4014XSAK/@@download/IGVFFI4014XSAK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/c55fb653-b443-4767-a293-c1bc7c9562e7/IGVFFI4014XSAK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3955WSPN/",
"accession": "IGVFFI3955WSPN",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_6.2bc25_TCCTTGGT_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:22:28.902357+00:00",
"file_format": "fastq",
"file_size": 641368823,
"href": "/sequence-files/IGVFFI3955WSPN/@@download/IGVFFI3955WSPN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/038ae130-4040-4e48-b40b-d59c13fbbf7f/IGVFFI3955WSPN.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_2PMDox1_6.2bc25_TCCTTGGT_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6132PXBN/",
"accession": "IGVFFI6132PXBN",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_6.2bc34_TCTGGCGA_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:22:54.410364+00:00",
"file_format": "fastq",
"file_size": 694912143,
"href": "/sequence-files/IGVFFI6132PXBN/@@download/IGVFFI6132PXBN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/a8ba7855-d04d-4125-8f44-877dad1e5b76/IGVFFI6132PXBN.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_2PMDox1_6.2bc34_TCTGGCGA_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5712MZTB/",
"accession": "IGVFFI5712MZTB",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_6.2bc35_AGGATCTA_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:23:03.215508+00:00",
"file_format": "fastq",
"file_size": 457369352,
"href": "/sequence-files/IGVFFI5712MZTB/@@download/IGVFFI5712MZTB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/680f4605-ab70-4de9-9125-bf6240996524/IGVFFI5712MZTB.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_2PMDox1_6.2bc35_AGGATCTA_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6559SZAD/",
"accession": "IGVFFI6559SZAD",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_6.2bc25_TCCTTGGT_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:22:37.197563+00:00",
"file_format": "fastq",
"file_size": 587046313,
"href": "/sequence-files/IGVFFI6559SZAD/@@download/IGVFFI6559SZAD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/752791ee-3402-47b5-baa2-9d66a0cc3143/IGVFFI6559SZAD.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_2PMDox1_6.2bc25_TCCTTGGT_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8066GKDM/",
"accession": "IGVFFI8066GKDM",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_6.2bc35_AGGATCTA_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:23:09.907814+00:00",
"file_format": "fastq",
"file_size": 410893723,
"href": "/sequence-files/IGVFFI8066GKDM/@@download/IGVFFI8066GKDM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/70f7f4d0-f115-4372-ac8e-b536079805d3/IGVFFI8066GKDM.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_2PMDox1_6.2bc35_AGGATCTA_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0864MICP/",
"accession": "IGVFFI0864MICP",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_6.2bc34_TCTGGCGA_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:22:45.223273+00:00",
"file_format": "fastq",
"file_size": 751519585,
"href": "/sequence-files/IGVFFI0864MICP/@@download/IGVFFI0864MICP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/00f511e2-d81a-461f-8c74-e35d906a9080/IGVFFI0864MICP.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_2PMDox1_6.2bc34_TCTGGCGA_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/IGVFDS0385ESBQ/",
"accession": "IGVFDS0385ESBQ",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_6"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9019CRXH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9019CRXH",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox1_6"
],
"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": "2024-02-06T21:22:19.616193+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "c53e88d7-307f-4adf-841b-dff5dd1e6fca"
}