MPRAu 3′UTR SNV/deletion tiling in HepG2
Genome-wide functional screen of 3′UTR variants uncovers causal variants for human disease and evolutionA secondary MPRAu tiling library tested 5-bp non-overlapping deletions across the 100-bp sequence and all single-nucleotide substitutions within ±10 bp of 80 tamVars, using both reference and alternate sequence backgrounds.
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
Episomal GFP 3′UTR reporter with random hexamer barcodes; the table combines the published 5-bp deletion-tile and ±10-bp SNV-tile result sheets for this cell type. Effects are DESeq2 RNA-over-plasmid log2 fold-changes relative to the corresponding unperturbed parent oligo.
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 · 16 definitions
- element_id
- Unique oligonucleotide identifier for the perturbed tiling construct.
- parent_oligo_id
- Identifier of the unperturbed reference or alternate parent oligo.
- perturbation_type
- 5bp_deletion or SNV substitution.
- offset_start
- Start position of the perturbation relative to the parent variant; negative is upstream.
- offset_end
- End position of the perturbation relative to the parent variant; negative is upstream.
- chromosome
- Source chromosome.
- strand
- Source oligo strand.
- genomic_start_hg19
- 1-based hg19 start coordinate of the deletion/SNV when supplied.
- genomic_end_hg19
- 1-based hg19 end coordinate of the deletion/SNV when supplied.
- base_substitution
- Base inserted at the SNV-tiled position; blank for deletion rows.
- effect_log2fc
- Published DESeq2 log2 fold-change of the perturbed oligo versus its unperturbed parent.
- effect_lfcse
- Published DESeq2 standard error for the tiling effect.
- effect_pvalue
- Published DESeq2 p-value for the tiling effect.
- effect_padj
- Published BH-adjusted p-value for the tiling effect.
- background_context
- Reference or alternate parent sequence context parsed from the parent oligo ID.
- qc_pass
- TRUE for rows with complete target-cell DESeq2 statistics retained in the package.
Quality control
The authors used the same barcode-flanking sequence, BWA alignment-score ≥0.95, multi-mapping, and DESeq2 processing framework as the main MPRAu screen. The supplied tiling sheets do not contain per-oligo plasmid counts, so this package retained measured deletion/SNV rows only when the target-cell log2FC, standard error, p-value, and BH-adjusted p-value were all present. 16761 of 16950 supplied deletion/SNV rows passed this completeness filter.
Curation notes
This is the study’s mechanistic follow-up library, not a GWAS table: it resolves sequence positions around 80 strong tamVars using deletion and SNV perturbations. Missing genomic coordinates are preserved as blank when the source tiling sheet reported NA.