MapUTR 3′ UTR RNA-editing stability MPRA in HEK293T cells
Cytosine-to-uracil RNA editing is upregulated by pro-inflammatory stimulation of myeloid cellsA library of 164-bp 3′ UTR oligonucleotides carrying either the reference or RNA-edited nucleotide was cloned into a reporter vector and electroporated into HEK293T cells. Three biological replicates were assayed by reporter RNA sequencing and plasmid DNA sequencing, and MPRAnalyze was used to compare edited-versus-reference RNA/DNA abundance.
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
Reference versus RNA-edited 3′ UTR reporter allele; no HEK293T inflammatory treatment reported
The MapUTR design uses paired 164-bp oligomers that differ at the nominated editing site and are cloned into a reporter vector. Reporter plasmids were electroporated into HEK293T cells; after 24 hours, reporter RNA and plasmid DNA libraries were sequenced, with DNA used to normalize RNA abundance. MPRAnalyze tested differential RNA/DNA signal between edited and unedited alleles across three biological replicates. LPS and IFNβ labels in the table describe the source monocyte cohorts in which sites were nominated, not separate HEK293T MPRA treatment arms.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 24 definitions
- element_id
- Unique RNA-editing site identifier from the authors' MPRA result, formatted as chromosome:1-based position:reference allele:edited allele.
- chromosome
- Chromosome parsed from element_id.
- position_grch38
- 1-based genomic position parsed from element_id; the paper's RNA-seq/editing coordinates use GRCh38.
- reference_allele
- Unedited nucleotide in the tested 3′ UTR reporter allele.
- edited_allele
- Nucleotide representing the RNA-edited reporter allele.
- editing_class
- Biological editing class inferred from the allele pair; A:G is A-to-I and C:T is C-to-U in this dataset.
- oligo_length_bp
- Length of each MapUTR library oligomer reported in the paper: 164 bp.
- library_site_count
- Number of source cohort/stimulation collections in which the editing site was identified, as supplied by the authors.
- source_cohorts
- Semicolon-delimited source cohorts in which the editing site was detected; 165 denotes the discovery cohort and 105 the replication cohort, with LPS or IFNb indicating stimulation.
- gene
- Gene annotation supplied with the authors' MPRA result.
- source_hg19_feature
- Feature coordinate supplied by the authors in an hg19-style column; retained verbatim and not used as the primary assay coordinate.
- library_subpool
- Authors' MPRA library subpool/batch label.
- log2fc_edited_vs_reference
- Authors' MPRA log2 fold-change for edited versus reference reporter RNA/DNA signal.
- neg_log10_fdr
- Authors' logP field, numerically corresponding to approximately −log10(FDR).
- test_statistic
- MPRAnalyze test statistic supplied by the authors.
- p_value
- Nominal P-value supplied by the authors for the edited-versus-reference MPRA comparison.
- fdr
- Multiple-testing-adjusted P-value supplied by the authors.
- source_significant
- Authors' Y/N significance call, normalized to true/false; 533 candidate sites were flagged true.
- stated_threshold_pass
- Derived true/false flag for FDR ≤ 0.1 and absolute log2 fold-change ≥ 0.1, the threshold stated in Methods.
- source_call_discrepancy
- True when the authors' source_significant flag disagrees with stated_threshold_pass.
- miRNA_seed_site_flag
- Authors' flag for whether the editing site was associated with a predicted miRNA seed-site analysis.
- miRNA_association_count
- Number of predicted miRNA associations for the site in the authors' miRNA result file.
- miRNA_names
- Semicolon-delimited predicted miRNA names associated with the site; blank when none were supplied.
- miRNA_effects
- Semicolon-delimited predicted miRNA effects (creation or disruption); blank when none were supplied.
Quality control
The authors used three biological replicates and MPRAnalyze for RNA/DNA-normalized allele comparisons. The methods state FDR ≤ 0.1 and |logFC| ≥ 0.1 for significance; the Results section also reports FDR < 0.05. For this package, the candidate-only author result file was retained only when the site ID was parseable and the result contained complete logFC, statistic, nominal P-value, FDR, subpool, gene, and feature fields. This retained 2,006 unique candidate sites. The broader author result file contained 528 negative controls, 389 positive controls, and 144 candidate rows with missing assay statistics; all 1,061 rows were excluded from the processed table. Both significant and nonsignificant complete candidate results were retained because nonsignificant assay outcomes are informative. No published per-barcode count threshold was available in the packaged files.
Curation notes
The processed table contains 2,006 unique complete candidate sites: 1,994 A-to-I (A:G) and 12 C-to-U (C:T), with 533 source-significant calls and 353 sites flagged in the miRNA analysis. Two source-significant rows have absolute log2 fold-change below 0.1 despite the stated Methods threshold; they were retained and marked in source_call_discrepancy because the source significance field was preserved. The official Supplementary Table 18 worksheet is retained in raw_data as a direct extract, but it contains discovery-cohort plotting rows with repeated site IDs and blank result cells; the candidate-only GitHub result was used for the one-row-per-site processed table. The Cellosaurus accession CVCL_0063 is normalized to the requested CURIE form CVCL:0063. Raw sequencing reads were not included.