{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5906WMBP/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5906WMBP",
"aliases": [
"jesse-engreitz:auxiliary_NOS3_CRISPRi_FF_R1_FFrep2_binA_PCR2_S201"
],
"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 [IGVFDS5906WMBP](/auxiliary-sets/IGVFDS5906WMBP/) has sequence file(s): [IGVFFI6550RJDC](/sequence-files/IGVFFI6550RJDC/), [IGVFFI6344IWJB](/sequence-files/IGVFFI6344IWJB/), [IGVFFI3380KZRH](/sequence-files/IGVFFI3380KZRH/) 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/IGVFDS5906WMBP/"
}
]
},
"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": "2024-04-15T23:17:13.899270+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/IGVFFI6550RJDC/",
"accession": "IGVFFI6550RJDC",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:38.753396+00:00",
"file_format": "fastq",
"file_size": 32655186,
"href": "/sequence-files/IGVFFI6550RJDC/@@download/IGVFFI6550RJDC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/16/850a19d8-63ea-424f-84b8-600d112df111/IGVFFI6550RJDC.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-BinA-PCRrep2_S201_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6344IWJB/",
"accession": "IGVFFI6344IWJB",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:41.757407+00:00",
"file_format": "fastq",
"file_size": 87230727,
"href": "/sequence-files/IGVFFI6344IWJB/@@download/IGVFFI6344IWJB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/16/c996bf9e-181e-4fa7-9670-a802c9d500c7/IGVFFI6344IWJB.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-BinA-PCRrep2_S201_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3380KZRH/",
"accession": "IGVFFI3380KZRH",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-16T21:43:40.232072+00:00",
"file_format": "fastq",
"file_size": 30010442,
"href": "/sequence-files/IGVFFI3380KZRH/@@download/IGVFFI3380KZRH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/16/b421c099-84b9-43b7-b114-72f3d5b1d4c2/IGVFFI3380KZRH.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-BinA-PCRrep2_S201_I2_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/IGVFDS3867YHHK/",
"accession": "IGVFDS3867YHHK",
"aliases": [
"jesse-engreitz:measurement_NOS3_CRISPRi_FF_R1_FFrep2_binA_PCR2_S201"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-06-22T00:27:09.743523+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8817SMTB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8817SMTB",
"aliases": [
"jesse-engreitz:in-vitro-system_NOS3_CRISPRi_FF_R1_FFrep2_binA_PCR2_S201"
],
"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 A for 0-25% 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": "2024-04-16T21:43:38.753396+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3",
"uuid": "46406e4d-9edf-40d6-8240-396507019c1d"
}