Human APA variant 3′ UTR MPRA

An episomal 3′ UTR APA reporter array measured ClinVar, ACMG/HGMD-associated, and saturation-mutagenesis SNVs in human polyadenylation-site contexts. The processed table preserves the repository’s measured variant effect, APARENT prediction, significance, and sequence annotations in one variant-level table.

Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0063
Reference genome: GRCh37
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The reporter is a transiently transfected episomal APA minigene. RNA-seq read distributions are summarized as measured log-odds effects for the alternative sequence, with cleavage/isoform usage as the readout; predicted effects from APARENT are retained for comparison.

Quality control

The repository export was already aggregated at the variant level and contained no barcode- or allele-level count columns. Retained rows with valid 164-nt A/C/G/T reference and alternate sequences and finite numeric measured effect, predicted effect, and p-value fields; all 13,792 source rows passed these available-data checks. The repository notebook’s stronger designed-MPRA filter (at least 5 barcodes per allele and mean total count ≥ 200 for both alleles) could not be independently reapplied because those fields are not present in this export.

Curation notes

The source export contains 13,792 rows, while the article narrative describes more than 12,000 (12,348 in the main text) measured variants. This package preserves the complete repository summary export after the available sequence/numeric QC; the discrepancy is retained as a provenance note rather than silently dropping rows. The article text/resource table uses HEK293/HEK293FT terminology, but the GEO sample records explicitly identify HEK293T; the biosample mapping follows GEO (CVCL:0063). The processed table is not a barcode-level reanalysis, so exact replicate/count QC from the source notebook cannot be reconstructed.

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Human APA variant 3′ UTR MPRA

Processed data

Quality control

Curation notes

Cite OpenMPRA

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