HEK293 3′UTR A-to-G RNA-editing MPRA
Widespread RNA hypoediting in schizophrenia and its relevance to mitochondrial functionA plasmid-based 3′UTR MPRA tested both unedited A and edited G versions of 770 differential A-to-G RNA-editing sites drawn from four postmortem schizophrenia cohorts. Oligos carrying 158-nt test sequences were cloned into the eGFP 3′UTR, electroporated into HEK293 cells, and assayed by matched plasmid-DNA and mRNA sequencing 24 hours after transfection across three biological replicates.
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.
Perturbation & assay details
Basal / Untreated
Twist Bioscience synthesized 200-nt oligos containing cloning adaptors and 158-nt test sequences centered on each editing site; boundary sites were adjusted to remain within the 3′UTR. The A (unedited) and G (edited) versions were cloned into the eGFP 3′UTR of master plasmids, electroporated into HEK293 cells, and harvested for RNA extraction 24 hours later. Test sequences were amplified from plasmid DNA and mRNA to make DNA-sequencing and RNA-seq libraries. MPRAnalyze compared the relative DNA and mRNA enrichment of the two allele constructs across three biological replicates.
Processed data
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 16 definitions
- editing_site
- Published genomic coordinate of the differential A-to-G editing site.
- chromosome
- Chromosome parsed from editing_site.
- position
- 1-based genomic position parsed from editing_site.
- gene_name
- Host gene named in Supplementary Table S3.
- cohort
- Postmortem brain cohort from which the differential editing site was selected: BrainGVEX, CMC, HBCC, or LIBD.
- unedited_allele
- A allele hard-coded into the unedited reporter construct.
- edited_allele
- G allele hard-coded into the edited reporter construct.
- ln_fold_change_g_vs_a
- Signed natural-log fold change for the edited G versus unedited A reporter comparison; positive values indicate higher reporter expression for G. This normalizes the source column labeled negative log FC, which contains signed values and matches the paper's ln(Fold Change) threshold.
- fold_change_g_vs_a
- Exponentiated ln_fold_change_g_vs_a, interpreted as edited-G reporter expression divided by unedited-A reporter expression.
- p_value
- MPRAnalyze p-value for the allele-dependent reporter effect.
- fdr
- MPRAnalyze FDR-adjusted p-value.
- neg_log10_fdr
- Negative base-10 logarithm of the FDR, carried through from Supplementary Table S3.
- significance
- Author-provided call: upregulated, downregulated, or NO.
- passes_author_significance_threshold
- Boolean recomputation of FDR ≤ 0.1 and absolute ln fold change ≥ 0.1.
- effect_direction
- Normalized direction label based on the author call and signed effect.
- source_table
- Provenance label for the source supplementary table.
Quality control
The authors reported three biological replicates with high inter-replicate correlation (R = 0.84) and used MPRAnalyze on matched plasmid DNA and expressed mRNA. Author significance required FDR ≤ 0.1 and absolute ln(Fold Change) ≥ 0.1. Supplementary Table S3 contains 770 testable sites with finite p-values, FDRs, and signed fold-change values; all 770 were retained because non-significant rows are valid tested outcomes and no per-element count or additional MPRA exclusion fields were released. The processed table recomputes the author threshold in passes_author_significance_threshold rather than filtering out non-significant measurements.
Curation notes
This is the study's one MPRA experiment; the MFN1 recoding, prime-editing, mitochondrial morphology, and apoptosis assays are non-MPRA follow-up experiments and were not packaged as MPRA experiments. The human reference assembly is not explicitly stated in the article or Table S3, so reference_genome is null and published coordinates are retained as-is. HEK293 was resolved to Cellosaurus CVCL:0045. The source table's column label negative log FC is anomalous because its values are signed and the paper describes the statistic as ln(Fold Change); the processed table labels it ln_fold_change_g_vs_a and records the source interpretation here. The paper does not release MPRA sequences, barcode-level counts, or replicate-level count matrices; the aggregate 770-site MPRAnalyze result table is the genuine MPRA data available for packaging.