{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9928OZTX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9928OZTX",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_RNA_BarcodeSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002675/",
"assay_slims": [
"reporter"
],
"status": "released",
"term_name": "massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9928OZTX](/measurement-sets/IGVFDS9928OZTX/) has sequence file(s) [IGVFFI4518NPFP](/sequence-files/IGVFFI4518NPFP/), [IGVFFI9536PJTO](/sequence-files/IGVFFI9536PJTO/), [IGVFFI2905AIKP](/sequence-files/IGVFFI2905AIKP/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS9928OZTX/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1073DKXV](/auxiliary-sets/IGVFDS1073DKXV/) has sequence file(s) [IGVFFI7244QLGY](/sequence-files/IGVFFI7244QLGY/), [IGVFFI4246ABNZ](/sequence-files/IGVFFI4246ABNZ/), [IGVFFI9339WALF](/sequence-files/IGVFFI9339WALF/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS1073DKXV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing read names",
"detail": "MPRA Measurement set [IGVFDS9928OZTX](/measurement-sets/IGVFDS9928OZTX/) links to sequence files: [IGVFFI4518NPFP](/sequence-files/IGVFFI4518NPFP/),[IGVFFI9536PJTO](/sequence-files/IGVFFI9536PJTO/),[IGVFFI2905AIKP](/sequence-files/IGVFFI2905AIKP/) that do not specify `read_names`. MPRA measurement set and auxiliary set sequence files are expected to specify a read name.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_MPRA_read_names",
"path": "/measurement-sets/IGVFDS9928OZTX/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9928OZTX](/measurement-sets/IGVFDS9928OZTX/) has sequence file(s): [IGVFFI4518NPFP](/sequence-files/IGVFFI4518NPFP/), [IGVFFI9536PJTO](/sequence-files/IGVFFI9536PJTO/), [IGVFFI2905AIKP](/sequence-files/IGVFFI2905AIKP/) which do not have a `seqspec_document`. Sequence files in a file set associated with non-single cell data are expected to link to a sequence specification document.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS9928OZTX/"
},
{
"category": "missing read names",
"detail": "MPRA Auxiliary set [IGVFDS1073DKXV](/auxiliary-sets/IGVFDS1073DKXV/) links to sequence files: [IGVFFI7244QLGY](/sequence-files/IGVFFI7244QLGY/),[IGVFFI4246ABNZ](/sequence-files/IGVFFI4246ABNZ/),[IGVFFI9339WALF](/sequence-files/IGVFFI9339WALF/) that do not specify `read_names`. MPRA measurement set and auxiliary set sequence files are expected to specify a read name.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_MPRA_read_names",
"path": "/auxiliary-sets/IGVFDS1073DKXV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1073DKXV](/auxiliary-sets/IGVFDS1073DKXV/) has sequence file(s): [IGVFFI7244QLGY](/sequence-files/IGVFFI7244QLGY/), [IGVFFI4246ABNZ](/sequence-files/IGVFFI4246ABNZ/), [IGVFFI9339WALF](/sequence-files/IGVFFI9339WALF/) which do not have a `seqspec_document`. Sequence files in a file set associated with non-single cell data are expected to link to a sequence specification document.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS1073DKXV/"
}
]
},
"auxiliary_sets": [
{
"@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"
}
],
"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": "2024-11-23T01:01:08.428611+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4518NPFP/",
"accession": "IGVFFI4518NPFP",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_RNA_BarcodeSequencing_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:10:16.288562+00:00",
"file_format": "fastq",
"file_size": 327772929,
"href": "/sequence-files/IGVFFI4518NPFP/@@download/IGVFFI4518NPFP.fastq.gz",
"md5sum": "3a33e60aca680ed82f2ff9595989caba",
"s3_uri": "s3://igvf-files/2024/11/23/93f2cba7-8554-47d4-bc31-fa810b96ebfe/IGVFFI4518NPFP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R2_RNA_S8_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9536PJTO/",
"accession": "IGVFFI9536PJTO",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_RNA_BarcodeSequencing_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:10:50.923549+00:00",
"file_format": "fastq",
"file_size": 359289890,
"href": "/sequence-files/IGVFFI9536PJTO/@@download/IGVFFI9536PJTO.fastq.gz",
"md5sum": "f81f6c0b1aeafe2431f3267512b76b49",
"s3_uri": "s3://igvf-files/2024/11/23/806720e2-87b4-45af-9c80-54a03dc9f435/IGVFFI9536PJTO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R2_RNA_S8_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2905AIKP/",
"accession": "IGVFFI2905AIKP",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_RNA_BarcodeSequencing_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:11:28.560425+00:00",
"file_format": "fastq",
"file_size": 326147813,
"href": "/sequence-files/IGVFFI2905AIKP/@@download/IGVFFI2905AIKP.fastq.gz",
"md5sum": "6113a7f81fef5cca1844ca1e45feea67",
"s3_uri": "s3://igvf-files/2024/11/23/890d10c4-82b5-4657-8187-c014cdc6caea/IGVFFI2905AIKP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R2_RNA_S8_R3_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1376WOXJ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "lentiMPRA",
"protocols": [
"https://www.protocols.io/view/massive-parallel-reporter-assay-mpra-kxygxpmkwl8j/v1"
],
"samples": [
{
"@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": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-23T01:08:42.346162+00:00",
"summary": "lentiMPRA integrating a reporter library targeting sequence variants in a genomic locus",
"uuid": "c60c063f-04de-4e20-ab76-ce27f39fb9af"
}