A two-library luciferase MPRA tested 145-bp reference, alternative, and scrambled sequences from 840 melanoma-associated variants in the UACC903 melanoma cell line. Enhancer and promoter configurations were transfected in two biological replicates per library/configuration, and barcode RNA/DNA activity was quantified.
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:4052
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
pMPRA1-derived episomal luc2 reporter. Each variant was represented by reference, alternative, and scrambled 21-bp-null constructs in forward and reverse orientations, with 10 random 10-bp barcodes per sequence. Enhancer constructs contained a minimal TATA promoter; promoter constructs lacked a promoter. Two Agilent oligo libraries were transfected into UACC903, harvested 24 hours later, and quantified by HiSeq2500 sequencing of DNA input and polyadenylated RNA output. The table retains library/configuration/strand-specific activity summaries and the paper's published variant-level annotations.
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 · 70 definitions
variant_id
Author-provided hg19 chromosome:coordinate identifier for the tested variant.
chromosome
hg19 chromosome.
position_hg19
1-based hg19 coordinate.
rs_id
dbSNP rs identifier joined from the paper's Supplementary Tables 5 and 8; blank when the paper did not provide one for the row's variant.
ref_allele
Reference allele used in the author variant list and construct labeled ref.
alt_allele
Alternative allele used in the author variant list and construct labeled alt.
variant_note
Author annotation distinguishing the 832 GWAS variants from the 8 negative controls.
published_mpra_significant
TRUE for variants listed in the paper's Supplementary Table 5 as significant MPRA variants; blank otherwise.
published_uacc_direction
Author-reported UACC903 direction of departure from the scrambled null for the significant-variant analysis.
published_uacc_allelic_log2_alt_vs_ref
Author-reported UACC903 allelic difference, log2(Alt/Ref), from Supplementary Table 5.
published_uacc_fdr_alt_vs_ref
Author-reported UACC903 Benjamini-Hochberg FDR for the Alt-versus-Ref comparison.
published_uacc_fdr_vs_scrambled
Author-reported smaller FDR for either allele's comparison with the scrambled null in UACC903.
published_combined_direction
Author-reported direction of departure from the scrambled null in the combined UACC903 and HEK293FT analysis.
published_combined_allelic_log2_alt_vs_ref
Author-reported combined-cell allelic difference, log2(Alt/Ref), from Supplementary Table 5.
published_combined_fdr_alt_vs_ref
Author-reported combined-cell Benjamini-Hochberg FDR for the Alt-versus-Ref comparison.
published_combined_fdr_vs_scrambled
Author-reported smaller FDR for either allele's comparison with the scrambled null in the combined analysis.
negative_control
TRUE for the eight author-designated high-LD negative-control variants.
library
Oligo library identifier, Library1 or Library2.
construct_class
Enhancer for the minimal-TATA construct or Promoter for the promoter-less construct.
promoter_configuration
Construct promoter design: minimal TATA promoter for enhancer testing or no promoter for promoter testing.
strand
Orientation of the tested 145-bp sequence: fwd or reverse-complement rev.
ref_sequence_145bp
145-bp sequence used for the reference-allele construct in this orientation.
alt_sequence_145bp
145-bp sequence used for the alternative-allele construct in this orientation.
scramble_sequence_145bp
145-bp sequence with the 21-bp variant-centered core scrambled to provide the null construct.
transfection_ids
GEO/author transfection IDs contributing to this cell/library/configuration row (T11-T18 for UACC903).
n_output_replicates
Number of UACC903 RNA-output biological transfection replicates summarized in the row.
ref_barcodes_designed
Number of unique reference barcode IDs represented in the processed workbook.
alt_barcodes_designed
Number of unique alternative barcode IDs represented in the processed workbook.
scramble_barcodes_designed
Number of unique scrambled-control barcode IDs represented in the processed workbook.
ref_barcodes_qc
Number of reference barcodes with inferred input DNA TPM >= 6.
alt_barcodes_qc
Number of alternative barcodes with inferred input DNA TPM >= 6.
scramble_barcodes_qc
Number of scrambled-control barcodes with inferred input DNA TPM >= 6.
ref_mean_dna_tpm_qc
Mean inferred input DNA TPM across denominator-QC reference barcodes.
alt_mean_dna_tpm_qc
Mean inferred input DNA TPM across denominator-QC alternative barcodes.
scramble_mean_dna_tpm_qc
Mean inferred input DNA TPM across denominator-QC scrambled barcodes.
ref_log2_rna_dna_rep1
Mean log2(RNA TPM/DNA TPM) across QC-passing reference barcodes in output replicate 1.
alt_log2_rna_dna_rep1
Mean log2(RNA TPM/DNA TPM) across QC-passing alternative barcodes in output replicate 1.
scramble_log2_rna_dna_rep1
Mean log2(RNA TPM/DNA TPM) across QC-passing scrambled barcodes in output replicate 1.
ref_mean_rna_tpm_rep1
Mean RNA-output TPM across QC-passing reference barcodes in output replicate 1.
alt_mean_rna_tpm_rep1
Mean RNA-output TPM across QC-passing alternative barcodes in output replicate 1.
scramble_mean_rna_tpm_rep1
Mean RNA-output TPM across QC-passing scrambled barcodes in output replicate 1.
ref_log2_rna_dna_rep2
Mean log2(RNA TPM/DNA TPM) across QC-passing reference barcodes in output replicate 2.
alt_log2_rna_dna_rep2
Mean log2(RNA TPM/DNA TPM) across QC-passing alternative barcodes in output replicate 2.
scramble_log2_rna_dna_rep2
Mean log2(RNA TPM/DNA TPM) across QC-passing scrambled barcodes in output replicate 2.
ref_mean_rna_tpm_rep2
Mean RNA-output TPM across QC-passing reference barcodes in output replicate 2.
alt_mean_rna_tpm_rep2
Mean RNA-output TPM across QC-passing alternative barcodes in output replicate 2.
scramble_mean_rna_tpm_rep2
Mean RNA-output TPM across QC-passing scrambled barcodes in output replicate 2.
ref_log2_rna_dna_rep3
Mean log2(RNA TPM/DNA TPM) across QC-passing reference barcodes in output replicate 3; blank when the condition had only two replicates.
alt_log2_rna_dna_rep3
Mean log2(RNA TPM/DNA TPM) across QC-passing alternative barcodes in output replicate 3; blank when the condition had only two replicates.
scramble_log2_rna_dna_rep3
Mean log2(RNA TPM/DNA TPM) across QC-passing scrambled barcodes in output replicate 3; blank when the condition had only two replicates.
ref_mean_rna_tpm_rep3
Mean RNA-output TPM across QC-passing reference barcodes in output replicate 3; blank when the condition had only two replicates.
alt_mean_rna_tpm_rep3
Mean RNA-output TPM across QC-passing alternative barcodes in output replicate 3; blank when the condition had only two replicates.
scramble_mean_rna_tpm_rep3
Mean RNA-output TPM across QC-passing scrambled barcodes in output replicate 3; blank when the condition had only two replicates.
ref_log2_rna_dna_rep4
Mean log2(RNA TPM/DNA TPM) across QC-passing reference barcodes in output replicate 4; blank when the condition had fewer than four replicates.
alt_log2_rna_dna_rep4
Mean log2(RNA TPM/DNA TPM) across QC-passing alternative barcodes in output replicate 4; blank when the condition had fewer than four replicates.
scramble_log2_rna_dna_rep4
Mean log2(RNA TPM/DNA TPM) across QC-passing scrambled barcodes in output replicate 4; blank when the condition had fewer than four replicates.
ref_mean_rna_tpm_rep4
Mean RNA-output TPM across QC-passing reference barcodes in output replicate 4; blank when the condition had fewer than four replicates.
alt_mean_rna_tpm_rep4
Mean RNA-output TPM across QC-passing alternative barcodes in output replicate 4; blank when the condition had fewer than four replicates.
scramble_mean_rna_tpm_rep4
Mean RNA-output TPM across QC-passing scrambled barcodes in output replicate 4; blank when the condition had fewer than four replicates.
ref_mean_log2_rna_dna
Mean of the replicate-level reference log2 RNA/DNA activity scores.
alt_mean_log2_rna_dna
Mean of the replicate-level alternative log2 RNA/DNA activity scores.
scramble_mean_log2_rna_dna
Mean of the replicate-level scrambled-null log2 RNA/DNA activity scores.
ref_geomean_rna_dna_ratio
Geometric mean RNA/DNA activity ratio for the reference construct, calculated as 2 to the ref_mean_log2_rna_dna power.
alt_geomean_rna_dna_ratio
Geometric mean RNA/DNA activity ratio for the alternative construct, calculated as 2 to the alt_mean_log2_rna_dna power.
scramble_geomean_rna_dna_ratio
Geometric mean RNA/DNA activity ratio for the scrambled null, calculated as 2 to the scramble_mean_log2_rna_dna power.
alt_minus_ref_log2_effect_mean
Mean across replicates of the alternative-minus-reference log2 RNA/DNA activity effect.
alt_minus_ref_log2_effect_sd
Sample standard deviation across biological replicates of the alternative-minus-reference log2 activity effect.
ref_minus_scramble_log2_effect_mean
Mean reference-minus-scrambled-null log2 activity effect across replicates.
alt_minus_scramble_log2_effect_mean
Mean alternative-minus-scrambled-null log2 activity effect across replicates.
qc_pass
TRUE because the row passed the package's paired-construct and denominator-QC filters.
Quality control
The authors reported removal of barcode observations at 10 reads or lower, removal of tags with input DNA TPM below 6, and high replicate concordance in UACC903 (Pearson r >= 0.935). Their MPRA calls required FDR < 0.01 for both allelic difference and departure from the scrambled null in UACC903 and in the combined analysis. For this package, DNA TPM was reconstructed for each barcode as Supplementary Data 7 TPM divided by its RNA/DNA Ratio; only finite observations with inferred DNA TPM >= 6 were used. Each output replicate had to contribute at least three such barcodes for each reference, alternative, and scrambled construct, and each retained row had at least three denominator-QC barcodes per construct and 10 designed barcodes. The resulting 3,922 rows (809 variants represented) are the only rows in table.csv; all have qc_pass=TRUE. The supplementary workbook lacks the raw read-count column, so the <=10-read criterion was not independently reapplied to the workbook summaries; the compact GEO quant archive with read counts is retained for audit.
Curation notes
The table is grouped by variant, library, promoter configuration, and strand; the four UACC903 output transfections are T11-T18, with two biological replicates per condition. The paper's primary UACC903 analysis dropped repeated variants from Library1 for some statistics, whereas this package keeps all QC-passing library/strand rows and repeats published variant-level annotations for context. The focal rs398206 maps to 21:42742036 (C>A); its author-reported UACC903 allelic effect is log2(Alt/Ref)=1.64 (approximately 3.10-fold), while this table exposes the corresponding library- and strand-specific summaries. GEO input filenames do not cleanly match the library-specific variant sets, so the published Supplementary Data 7 TPM/Ratio values are the quantitative source for this table and the GEO quant archive is retained for audit.