{
"@context": "/terms/",
"@id": "/construct-library-sets/IGVFDS3011TBLW/",
"@type": [
"ConstructLibrarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3011TBLW",
"aliases": [
"jesse-engreitz:PPIF_promoter_lentiMPRA-ReporterLibrarySequencing"
],
"applied_to_samples": [
{
"@id": "/in-vitro-systems/IGVFSM6934LXGU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6934LXGU",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep1"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"nucleic_acid_delivery": "lentiviral transduction",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line transduced (lentivirus) with a reporter library"
},
{
"@id": "/in-vitro-systems/IGVFSM9869SECP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9869SECP",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"nucleic_acid_delivery": "lentiviral transduction",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line transduced (lentivirus) with a reporter library"
},
{
"@id": "/in-vitro-systems/IGVFSM5454DSMW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5454DSMW",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"nucleic_acid_delivery": "lentiviral transduction",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line transduced (lentivirus) with a reporter library"
}
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Construct library set [IGVFDS3011TBLW](/construct-library-sets/IGVFDS3011TBLW/) has sequence file(s): [IGVFFI8883UDHM](/sequence-files/IGVFFI8883UDHM/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/construct-library-sets/IGVFDS3011TBLW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing plasmid map",
"detail": "Construct library set [IGVFDS3011TBLW](/construct-library-sets/IGVFDS3011TBLW/) does not have a plasmid map attached in `documents`. Construct library sets are expected to be associated with a plasmid map document.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_construct_library_set_plasmid_map",
"path": "/construct-library-sets/IGVFDS3011TBLW/"
},
{
"category": "missing MPRA sequence designs",
"detail": "Construct library set [IGVFDS3011TBLW](/construct-library-sets/IGVFDS3011TBLW/) has no `integrated_content_files`. Reporter libraries used in MPRA assays are expected to link to an integrated content file of MPRA sequence designs.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_integrated_content_files",
"path": "/construct-library-sets/IGVFDS3011TBLW/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"control_for": [],
"creation_timestamp": "2024-11-22T22:40:43.339897+00:00",
"file_set_type": "reporter library",
"files": [
{
"@id": "/sequence-files/IGVFFI8883UDHM/",
"accession": "IGVFFI8883UDHM",
"aliases": [
"jesse-engreitz:PPIF_promoter_lentiMPRA_CRS-BC_Assignment_Sequencing"
],
"content_type": "reads",
"file_format": "fastq",
"href": "/sequence-files/IGVFFI8883UDHM/@@download/IGVFFI8883UDHM.fastq.gz",
"status": "preview",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1003XTAF/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"schema_version": "10",
"scope": "loci",
"selection_criteria": [
"sequence variants"
],
"small_scale_loci_list": [
{
"assembly": "GRCh38",
"chromosome": "chr10",
"end": 79347779,
"start": 79347211
}
],
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-23T00:44:33.281818+00:00",
"summary": "reporter library targeting sequence variants in a genomic locus",
"uuid": "caa12b32-2f64-4bfb-b000-3d9e53facaa4"
}