{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4697CFEN/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4697CFEN",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_6"
],
"audit": {
"INTERNAL_ACTION": [
{
"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/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4697CFEN](/auxiliary-sets/IGVFDS4697CFEN/) has sequence file(s): [IGVFFI5894VLNQ](/sequence-files/IGVFFI5894VLNQ/), [IGVFFI2943FXTE](/sequence-files/IGVFFI2943FXTE/), [IGVFFI0738KGIZ](/sequence-files/IGVFFI0738KGIZ/), [IGVFFI8137NKZA](/sequence-files/IGVFFI8137NKZA/) 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/IGVFDS4697CFEN/"
}
]
},
"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": "2024-02-06T19:29:35.078803+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",
"files": [
{
"@id": "/sequence-files/IGVFFI5894VLNQ/",
"accession": "IGVFFI5894VLNQ",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_6.2_CGCTCATT_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:20:07.052121+00:00",
"file_format": "fastq",
"file_size": 345328466,
"href": "/sequence-files/IGVFFI5894VLNQ/@@download/IGVFFI5894VLNQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/0a7caeca-f8d0-4f80-8233-9df562fa4f67/IGVFFI5894VLNQ.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_6.2_CGCTCATT_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2943FXTE/",
"accession": "IGVFFI2943FXTE",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_6_CGCTCATT_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:19:59.849998+00:00",
"file_format": "fastq",
"file_size": 473506726,
"href": "/sequence-files/IGVFFI2943FXTE/@@download/IGVFFI2943FXTE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/989f18ee-3f13-44f9-b5e8-3bed2a063d7a/IGVFFI2943FXTE.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_6_CGCTCATT_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0738KGIZ/",
"accession": "IGVFFI0738KGIZ",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_6_CGCTCATT_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:19:53.587888+00:00",
"file_format": "fastq",
"file_size": 411110449,
"href": "/sequence-files/IGVFFI0738KGIZ/@@download/IGVFFI0738KGIZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/9194d81e-f7d4-4634-ad6e-ef125faf6ede/IGVFFI0738KGIZ.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_6_CGCTCATT_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8137NKZA/",
"accession": "IGVFFI8137NKZA",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_11AMDox_6.2_CGCTCATT_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:20:12.693088+00:00",
"file_format": "fastq",
"file_size": 332709579,
"href": "/sequence-files/IGVFFI8137NKZA/@@download/IGVFFI8137NKZA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/4dd430a2-c12c-4292-a38b-97cb599c96f9/IGVFFI8137NKZA.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_6.2_CGCTCATT_L001_R2_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/IGVFDS2630GWQK/",
"accession": "IGVFDS2630GWQK",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_6"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3814HZQI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3814HZQI",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_11AMDox_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": "2024-02-06T21:19:53.587888+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "b85f80ce-aa9e-4de1-8cfd-acb915ff9144"
}