PASSPORT-seq 100-mirSNP assay-development library in HEK293
PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target SitesThe 200-construct library contained reference and alternate 63-nt miRNA-binding-site inserts for 100 mirSNPs. The pooled pIS-0 3′-UTR reporter was transiently transfected into HEK293 and five biological replicates were quantified by barcode sequencing relative to four plasmid-input 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
The pooled pIS-0 plasmid placed a 63-nt synthetic SNP-centered fragment in the firefly luciferase 3′ UTR. Reference and alternate constructs were transiently transfected, and barcode amplicon sequencing of cDNA was corrected by four plasmid-input replicates to quantify relative mRNA expression; protein translation was intentionally not measured.
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 · 13 definitions
- variant_id
- Stable package identifier combining the source rsID and reference/alternate alleles.
- source_row
- Row number in the corresponding processed supplementary source table.
- rsid
- dbSNP reference SNP identifier.
- reference_allele
- Reference allele used in the reporter construct.
- alternate_allele
- Alternate/variant allele used in the reporter construct.
- gene
- Gene or genes whose 3′ UTR contains the tested site.
- predicted_mirna_binding_sites
- Predicted miRNA-binding-site annotation extracted from the source reference/variant columns; when PDF column boundaries were not recoverable, reference and variant annotations are concatenated in source order.
- variant_percent_change
- Source percent change in reporter mRNA expression for the alternate allele relative to the reference allele in this cell line.
- mpra_fdr_p_value
- BH-adjusted edgeR PASSPORT-seq p-value for alternate-versus-reference expression; blank where the source does not report a numeric value.
- mpra_significant_fdr_0_05
- Whether the reported MPRA BH-adjusted p-value is below 0.05; blank when no numeric p-value is available.
- effect_direction
- Derived direction from variant_percent_change: alternate_increases, alternate_decreases, or no_change.
- library
- Library/analysis arm represented by this experiment.
- source_table
- Supplementary table used as the primary source.
Quality control
Publication QC included Sanger sequencing of 28 colonies, mapping-quality >20, perfect barcodes at both ends, four plasmid-input replicates for input correction, edgeR negative-binomial modeling with biological replicate/run and genotype covariates, and Benjamini–Hochberg FDR correction. Package QC retained rows with a valid rsID, single-nucleotide A/C/G/T reference and alternate alleles, nonempty gene, and finite HEK293 percent change; 100/100 rows passed. Numeric MPRA FDR values are populated only where Supplementary Table 3 reports them.
Curation notes
The paper reports 100 mirSNPs tested as 200 reference/alternate constructs and five biological replicates per cell line across two sequencing runs. Supplementary Table 1 encodes significance with PDF colors, while Supplementary Table 3 supplies numeric BH-adjusted p-values only for seven variants; unreported p-values are blank. The predicted-miRNA field preserves concatenated source annotations when the PDF did not expose the two source columns separately. The separate luciferase validation is not included in this MPRA table; the source does not specify a reference genome assembly, so reference_genome and region_of_interest are null.