{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM9869SECP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9869SECP",
"age": "unknown",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2"
],
"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"
},
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS3011TBLW/",
"accession": "IGVFDS3011TBLW",
"file_set_type": "reporter library",
"status": "preview"
}
],
"creation_timestamp": "2024-11-23T00:56:35.249660+00:00",
"demultiplexed_to": [],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"status": "released"
}
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS9928OZTX/",
"accession": "IGVFDS9928OZTX",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_RNA_BarcodeSequencing"
],
"file_set_type": "experimental data",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "lentiMPRA",
"status": "preview",
"summary": "lentiMPRA integrating a reporter library targeting sequence variants in a genomic locus"
},
{
"@id": "/auxiliary-sets/IGVFDS1073DKXV/",
"accession": "IGVFDS1073DKXV",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_DNA_BarcodeSequencing"
],
"file_set_type": "quantification DNA barcode sequencing",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "preview",
"summary": "quantification DNA barcode sequencing for lentiMPRA integrating a reporter library targeting sequence variants in a genomic locus"
},
{
"@id": "/analysis-sets/IGVFDS1376WOXJ/",
"accession": "IGVFDS1376WOXJ",
"aliases": [
"jesse-engreitz:PPIF_promoter_lentiMPRA_MPRAsnakeflow_analysis"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "preview",
"summary": "lentiMPRA: reporter experiment"
},
{
"@id": "/analysis-sets/IGVFDS1282YUKL/",
"accession": "IGVFDS1282YUKL",
"aliases": [
"jesse-engreitz:PPIF_promoter_lentiMPRA_mpralm_analysis"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "preview",
"summary": "lentiMPRA: reporter variants"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"multiplexed_in": [],
"nucleic_acid_delivery": "lentiviral transduction",
"origin_of": [],
"originated_from": {
"@id": "/in-vitro-systems/IGVFSM8319WNYW/",
"accession": "IGVFSM8319WNYW",
"status": "preview"
},
"parts": [],
"pooled_in": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"schema_version": "26",
"sex": "male",
"sorted_fractions": [],
"sources": [
{
"@id": "/sources/atcc/",
"status": "released",
"title": "ATCC"
}
],
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"summary": "Homo sapiens (male) THP-1 cell line transduced (lentivirus) with a reporter library",
"taxa": "Homo sapiens",
"uuid": "17820cd8-bcc9-4209-811d-1ad41f1ad9bb",
"virtual": false
}