{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS1376WOXJ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1376WOXJ",
"aliases": [
"jesse-engreitz:PPIF_promoter_lentiMPRA_MPRAsnakeflow_analysis"
],
"assay_titles": [
"lentiMPRA"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI7721GQHJ](/tabular-files/IGVFFI7721GQHJ/) has no `file_format_specifications`. Tabular files, with the exception of vcf files, are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI7721GQHJ/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS3011TBLW/",
"accession": "IGVFDS3011TBLW",
"file_set_type": "reporter library",
"status": "preview",
"summary": "reporter library targeting sequence variants in a genomic locus"
}
],
"control_for": [],
"creation_timestamp": "2024-11-23T01:21:36.987045+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI7721GQHJ/",
"accession": "IGVFFI7721GQHJ",
"aliases": [
"jesse-engreitz:PPIF_promoter_lentiMPRA_MPRAsnakeflow_results_file"
],
"content_type": "reporter experiment",
"controlled_access": false,
"creation_timestamp": "2024-12-11T18:48:05.236228+00:00",
"file_format": "tsv",
"file_size": 51400,
"href": "/tabular-files/IGVFFI7721GQHJ/@@download/IGVFFI7721GQHJ.tsv.gz",
"s3_uri": "s3://igvf-files/2024/12/11/9c893a8e-f5f0-4a81-bae8-3a1a0bc854e1/IGVFFI7721GQHJ.tsv.gz",
"status": "preview",
"submitted_file_name": "PPIF_promoter_lentiMPRA_MPRAsnakeflow_results.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7292KWHE/",
"accession": "IGVFDS7292KWHE",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep1_DNA_BarcodeSequencing"
],
"file_set_type": "quantification DNA barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1073DKXV/",
"accession": "IGVFDS1073DKXV",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_DNA_BarcodeSequencing"
],
"file_set_type": "quantification DNA barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3584HARV/",
"accession": "IGVFDS3584HARV",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3_DNA_BarcodeSequencing"
],
"file_set_type": "quantification DNA barcode sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2207IIRU/",
"accession": "IGVFDS2207IIRU",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep1_RNA_BarcodeSequencing"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9928OZTX/",
"accession": "IGVFDS9928OZTX",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_RNA_BarcodeSequencing"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8533DISB/",
"accession": "IGVFDS8533DISB",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3_RNA_BarcodeSequencing"
],
"file_set_type": "experimental data",
"status": "preview"
}
],
"input_for": [
"/analysis-sets/IGVFDS1282YUKL/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"protocols": [
"https://www.protocols.io/view/massive-parallel-reporter-assay-mpra-kxygxpmkwl8j/v1"
],
"sample_summary": "Homo sapiens THP-1 cell line, transfected with a reporter library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5454DSMW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5454DSMW",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line transduced (lentivirus) with a reporter library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM6934LXGU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6934LXGU",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep1"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line transduced (lentivirus) with a reporter library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9869SECP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9869SECP",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line transduced (lentivirus) with a reporter library",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-11T18:48:05.236228+00:00",
"summary": "lentiMPRA: reporter experiment",
"uuid": "519a6c97-d4bb-4f1e-9e50-571a58f88958",
"workflows": [
{
"@id": "/workflows/IGVFWF6032PEGT/",
"accession": "IGVFWF6032PEGT",
"name": "MPRAsnakeflow",
"status": "released",
"uniform_pipeline": true
}
]
}