{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1073DKXV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1073DKXV",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_DNA_BarcodeSequencing"
],
"audit": {
"INTERNAL_ACTION": [
{
"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/"
},
{
"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 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/IGVFDS1073DKXV/"
}
],
"NOT_COMPLIANT": [
{
"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/"
}
]
},
"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": "2024-11-23T00:59:54.801783+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "quantification DNA barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI7244QLGY/",
"accession": "IGVFFI7244QLGY",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_DNA_BarcodeSequencing_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:09:11.682419+00:00",
"file_format": "fastq",
"file_size": 34467934,
"href": "/sequence-files/IGVFFI7244QLGY/@@download/IGVFFI7244QLGY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/382229b4-4c03-4c8c-80b5-0d999b9e2f67/IGVFFI7244QLGY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "preview",
"submitted_file_name": "PPIF3_R2_DNA_S17_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4246ABNZ/",
"accession": "IGVFFI4246ABNZ",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_DNA_BarcodeSequencing_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:08:42.346162+00:00",
"file_format": "fastq",
"file_size": 32031358,
"href": "/sequence-files/IGVFFI4246ABNZ/@@download/IGVFFI4246ABNZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/7601390d-f801-4476-8821-96da042e1e45/IGVFFI4246ABNZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "preview",
"submitted_file_name": "PPIF3_R2_DNA_S17_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9339WALF/",
"accession": "IGVFFI9339WALF",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_DNA_BarcodeSequencing_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:09:40.514396+00:00",
"file_format": "fastq",
"file_size": 32004097,
"href": "/sequence-files/IGVFFI9339WALF/@@download/IGVFFI9339WALF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/bc59d92b-025e-4d65-b857-5ee947b8b206/IGVFFI9339WALF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"status": "preview",
"submitted_file_name": "PPIF3_R2_DNA_S17_R3_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1376WOXJ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9928OZTX/",
"accession": "IGVFDS9928OZTX",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep2_RNA_BarcodeSequencing"
],
"preferred_assay_title": "lentiMPRA",
"status": "preview"
}
],
"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": "12",
"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": "quantification DNA barcode sequencing for lentiMPRA integrating a reporter library targeting sequence variants in a genomic locus",
"uuid": "ecb114a7-db7d-43a7-81a0-503e09710ef9"
}