Experiment / E8RPENGKN3' UTR / RNA Stability MPRA (MPRAu)

PC3 IVT mRNA 3′ UTR stability MPRA

Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3′ untranslated region mutations

A fully capped and polyadenylated in-vitro-transcribed reporter mRNA library carrying paired 201-bp wild-type and mutant human 3′ UTR fragments was transfected into PC3 cells. Six biological replicates were sampled at 1, 3, 6, 12, and 24 hours to quantify allele-specific RNA decay and stability.

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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:0035
Reference genome: GRCh38
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The library was produced from the MPRA plasmid template using an integrated T7 promoter, capped and polyadenylated by in-vitro transcription, and normalized with an exogenous spike-in. Six PC3 replicates were sequenced at five time points; the publication fit nonlinear decay curves and used 1-to-3-hour and 1-to-6-hour decay comparisons. The processed table reports GEO normalized log2-CPM means, paired decay contrasts, and a package-derived log-linear half-life proxy rather than the authors’ fitted half-lives.

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 · 39 definitions

variant_id: Coordinate and REF-ALT identifier for the tested mutation.
chromosome: Chromosome parsed from variant_id.
position_grch38: 1-based GRCh38 coordinate parsed from variant_id.
reference_allele: Reference allele in the variant identifier.
alternate_allele: Alternate allele in the variant identifier.
wt_utr_sequence_201bp: 201-bp wild-type 3′ UTR insert sequence.
mutant_utr_sequence_201bp: 201-bp mutant 3′ UTR insert sequence.
replicate_count: Number of biological replicates summarized.
wt_mean_1hr_log2_cpm: Mean WT normalized log2 CPM at 1 hour.
mutant_mean_1hr_log2_cpm: Mean mutant normalized log2 CPM at 1 hour.
wt_mean_3hr_log2_cpm: Mean WT normalized log2 CPM at 3 hours.
mutant_mean_3hr_log2_cpm: Mean mutant normalized log2 CPM at 3 hours.
wt_mean_6hr_log2_cpm: Mean WT normalized log2 CPM at 6 hours.
mutant_mean_6hr_log2_cpm: Mean mutant normalized log2 CPM at 6 hours.
wt_mean_12hr_log2_cpm: Mean WT normalized log2 CPM at 12 hours.
mutant_mean_12hr_log2_cpm: Mean mutant normalized log2 CPM at 12 hours.
wt_mean_24hr_log2_cpm: Mean WT normalized log2 CPM at 24 hours.
mutant_mean_24hr_log2_cpm: Mean mutant normalized log2 CPM at 24 hours.
wt_1_to_3_decay_log2: WT mean 3-hour minus 1-hour normalized log2 CPM; more negative indicates greater loss.
mutant_1_to_3_decay_log2: Mutant mean 3-hour minus 1-hour normalized log2 CPM.
variant_effect_1_to_3_decay_log2: Mean paired mutant-minus-WT 1-to-3-hour decay contrast; positive indicates relatively greater mutant stability.
effect_1_to_3_sd: Sample standard deviation of the six paired 1-to-3-hour contrasts.
effect_1_to_3_p_value: Package-derived two-sided paired t-test p-value across six replicate contrasts.
effect_1_to_3_fdr: Benjamini-Hochberg FDR across retained variants for the package-derived 1-to-3-hour p-values.
significant_fdr_0_10_1_to_3: Whether package-derived 1-to-3-hour FDR is below 0.10.
wt_1_to_6_decay_log2: WT mean 6-hour minus 1-hour normalized log2 CPM.
mutant_1_to_6_decay_log2: Mutant mean 6-hour minus 1-hour normalized log2 CPM.
variant_effect_1_to_6_decay_log2: Mean paired mutant-minus-WT 1-to-6-hour decay contrast; positive indicates relatively greater mutant stability.
effect_1_to_6_sd: Sample standard deviation of the six paired 1-to-6-hour contrasts.
effect_1_to_6_p_value: Package-derived two-sided paired t-test p-value across six replicate contrasts.
effect_1_to_6_fdr: Benjamini-Hochberg FDR across retained variants for the package-derived 1-to-6-hour p-values.
significant_fdr_0_10_1_to_6: Whether package-derived 1-to-6-hour FDR is below 0.10.
wt_loglinear_decay_slope_log2_per_hour: Slope from a linear fit of WT mean normalized log2 CPM against 1, 3, 6, 12, and 24 hours.
mutant_loglinear_decay_slope_log2_per_hour: Slope from the analogous mutant time-course fit.
variant_effect_decay_slope_log2_per_hour: Mutant minus WT log-linear decay-slope effect; positive indicates a less negative mutant slope.
wt_loglinear_half_life_proxy_hours: Package-derived proxy of -1/slope for a negative WT slope; not the authors’ nonlinear fitted half-life.
mutant_loglinear_half_life_proxy_hours: Package-derived proxy of -1/slope for a negative mutant slope; not the authors’ nonlinear fitted half-life.
package_qc_pass: Always true because rows failing package QC were filtered out.
source_dataset: GEO source matrix and normalization used for this row.

Quality control

The authors used an exogenous spike-in, assessed replicate correlation and uniform library depth, and applied read-count and fitted-half-life filters in their stability analysis. Package QC retained only variant pairs with valid 201-bp WT/mutant oligos, complete finite values at all five time points across all six WT and mutant replicates, and mean normalized 1-hour log2 CPM ≥ 1 for both alleles; 6,347 rows passed. Non-significant but measured variants remain.

Curation notes

The IVT matrix contains 6,774 WT and 6,774 mutant allele rows; 6,347 paired variant IDs passed the package baseline and completeness filters and joined to paired oligos. The released file contains normalized log2 CPM rather than raw counts or the authors’ nonlinear fit output. The decay contrasts, paired p-values/FDR, and log-linear half-life proxies are therefore package-derived summary fields; the raw five-time-point allele means are retained for reanalysis.

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