{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2207IIRU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2207IIRU",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep1_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": "Auxiliary set [IGVFDS7292KWHE](/auxiliary-sets/IGVFDS7292KWHE/) has sequence file(s) [IGVFFI4195XWOV](/sequence-files/IGVFFI4195XWOV/), [IGVFFI3258ZIPG](/sequence-files/IGVFFI3258ZIPG/), [IGVFFI2302GGYX](/sequence-files/IGVFFI2302GGYX/) 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/IGVFDS7292KWHE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7292KWHE](/auxiliary-sets/IGVFDS7292KWHE/) has sequence file(s): [IGVFFI4195XWOV](/sequence-files/IGVFFI4195XWOV/), [IGVFFI3258ZIPG](/sequence-files/IGVFFI3258ZIPG/), [IGVFFI2302GGYX](/sequence-files/IGVFFI2302GGYX/) 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": "/auxiliary-sets/IGVFDS7292KWHE/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2207IIRU](/measurement-sets/IGVFDS2207IIRU/) has sequence file(s) [IGVFFI7129JGHL](/sequence-files/IGVFFI7129JGHL/), [IGVFFI8618TEYN](/sequence-files/IGVFFI8618TEYN/), [IGVFFI7703MSOV](/sequence-files/IGVFFI7703MSOV/) 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/IGVFDS2207IIRU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2207IIRU](/measurement-sets/IGVFDS2207IIRU/) has sequence file(s): [IGVFFI7129JGHL](/sequence-files/IGVFFI7129JGHL/), [IGVFFI8618TEYN](/sequence-files/IGVFFI8618TEYN/), [IGVFFI7703MSOV](/sequence-files/IGVFFI7703MSOV/) 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": "/measurement-sets/IGVFDS2207IIRU/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing read names",
"detail": "MPRA Auxiliary set [IGVFDS7292KWHE](/auxiliary-sets/IGVFDS7292KWHE/) links to sequence files: [IGVFFI4195XWOV](/sequence-files/IGVFFI4195XWOV/),[IGVFFI3258ZIPG](/sequence-files/IGVFFI3258ZIPG/),[IGVFFI2302GGYX](/sequence-files/IGVFFI2302GGYX/) 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/IGVFDS7292KWHE/"
},
{
"category": "missing read names",
"detail": "MPRA Measurement set [IGVFDS2207IIRU](/measurement-sets/IGVFDS2207IIRU/) links to sequence files: [IGVFFI7129JGHL](/sequence-files/IGVFFI7129JGHL/),[IGVFFI8618TEYN](/sequence-files/IGVFFI8618TEYN/),[IGVFFI7703MSOV](/sequence-files/IGVFFI7703MSOV/) 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/IGVFDS2207IIRU/"
}
]
},
"auxiliary_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"
}
],
"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": "2024-11-23T01:01:07.428455+00:00",
"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/IGVFFI7129JGHL/",
"accession": "IGVFFI7129JGHL",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep1_RNA_BarcodeSequencing_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:10:39.560770+00:00",
"file_format": "fastq",
"file_size": 346178154,
"href": "/sequence-files/IGVFFI7129JGHL/@@download/IGVFFI7129JGHL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/41cd9184-7304-4726-8f24-daa36a0bc25c/IGVFFI7129JGHL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R1_RNA_S7_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8618TEYN/",
"accession": "IGVFFI8618TEYN",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep1_RNA_BarcodeSequencing_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:10:00.416540+00:00",
"file_format": "fastq",
"file_size": 322668582,
"href": "/sequence-files/IGVFFI8618TEYN/@@download/IGVFFI8618TEYN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/90a12b01-eb59-45ca-8965-7ca67adf1995/IGVFFI8618TEYN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R1_RNA_S7_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7703MSOV/",
"accession": "IGVFFI7703MSOV",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep1_RNA_BarcodeSequencing_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:11:13.309943+00:00",
"file_format": "fastq",
"file_size": 321117051,
"href": "/sequence-files/IGVFFI7703MSOV/@@download/IGVFFI7703MSOV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/2e5c5aff-648f-4b0a-b406-87af2872edb1/IGVFFI7703MSOV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R1_RNA_S7_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/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"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-23T01:08:32.644433+00:00",
"summary": "lentiMPRA integrating a reporter library targeting sequence variants in a genomic locus",
"uuid": "d9692771-14e7-4fac-8102-e89dc7842a45"
}