{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0482NAKZ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0482NAKZ",
"aliases": [
"jesse-engreitz:auxiliary_NOS3_CRISPRi_FF_R1_FFrep2_binC_PCR1_S123"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0482NAKZ](/auxiliary-sets/IGVFDS0482NAKZ/) has sequence file(s): [IGVFFI0296ZMGR](/sequence-files/IGVFFI0296ZMGR/), [IGVFFI7211LNLZ](/sequence-files/IGVFFI7211LNLZ/), [IGVFFI8497XDEO](/sequence-files/IGVFFI8497XDEO/) 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/IGVFDS0482NAKZ/"
},
{
"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": "2024-04-15T23:17:10.882703+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/IGVFFI0296ZMGR/",
"accession": "IGVFFI0296ZMGR",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:30.623718+00:00",
"file_format": "fastq",
"file_size": 9554779,
"href": "/sequence-files/IGVFFI0296ZMGR/@@download/IGVFFI0296ZMGR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/16/ab4d2039-ff39-46ee-a53a-ffda38e597e1/IGVFFI0296ZMGR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0004205/",
"status": "released",
"submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep2-BinC-PCRrep1_S123_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7211LNLZ/",
"accession": "IGVFFI7211LNLZ",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:28.930414+00:00",
"file_format": "fastq",
"file_size": 9595835,
"href": "/sequence-files/IGVFFI7211LNLZ/@@download/IGVFFI7211LNLZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/16/8dcbd90b-26b6-4e81-9225-a565ad5808d6/IGVFFI7211LNLZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0004205/",
"status": "released",
"submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep2-BinC-PCRrep1_S123_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8497XDEO/",
"accession": "IGVFFI8497XDEO",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:32.031649+00:00",
"file_format": "fastq",
"file_size": 26892020,
"href": "/sequence-files/IGVFFI8497XDEO/@@download/IGVFFI8497XDEO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/16/06cb1bcc-708a-4ead-a0b9-e8656766f77e/IGVFFI8497XDEO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0004205/",
"status": "released",
"submitted_file_name": "/Desktop/NOS3/NOS3_CRISPRi_FlowFISH/231215S023-TeloHAEC-P219-Amp_NOS3-BioRep1-FFrep2-BinC-PCRrep1_S123_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7917YHKA/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2981PDKI/",
"accession": "IGVFDS2981PDKI",
"aliases": [
"jesse-engreitz:measurement_NOS3_CRISPRi_FF_R1_FFrep2_binC_PCR1_S123"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-06-22T00:27:16.677223+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7665HTFX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7665HTFX",
"aliases": [
"jesse-engreitz:in-vitro-system_NOS3_CRISPRi_FF_R1_FFrep2_binC_PCR1_S123"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS8953DFJK/"
],
"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": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin C for 51-75% expression of NOS3) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-04-16T21:43:28.930414+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3",
"uuid": "c5639f46-b1fa-4fc4-a086-d471a1cabec4"
}