The follow-up episomal MPRA tested original, HNF1-motif-deleted, and dinucleotide-shuffled fragments selected from the first library, with reference and alternate alleles where applicable. The table contains the 379 finite fragment/promoter records in publisher Table S15 for INS and SCP1 contexts in INS-1 832/13 cells, including five replicate log2 RNA/DNA values.
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
NCBITaxon:10116
Taxonomy ID
NCBITaxon:10116
Biosample
CVCL:7226
Reference genome
hg38
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
No exogenous treatment; transient electroporation and 24-hour reporter expression
Modified pMPRA1 episomal reporter with all fragments cloned upstream of the promoter and GFP reporter; the focused library used the INS or SCP1 promoter, original/deleted/dinucleotide-shuffled HNF1 motif designs, and reference/alternate alleles. Five RNA biological replicates and one plasmid-input DNA library were sequenced with UMI-bearing reporter transcripts. MPRAnalyze activity estimates were supplemented by per-fragment Wilcoxon comparisons in the paper; the processed table preserves author Table S15 scores and replicate log2(RNA/DNA) values.
Processed data
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Visible columns (33 of 33)
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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 · 33 definitions
fragment_id
Unique promoter-specific fragment identifier from publisher Table S15.
fragment_set_id
Identifier grouping the same target variant, fragment allele, and variant-position context across original, deleted, and shuffled designs.
promoter
Promoter paired with the fragment: INS or SCP1.
rsid
Target variant identifier; NA denotes a negative-control record.
chromosome
Chromosome of the target fragment in hg38.
position_hg38
Focal variant position in hg38.
reference_allele
Reference allele used for the target variant.
alternate_allele
Alternate allele used for the target variant.
fragment_allele
Allele carried by the fragment: R, A, or NA for controls.
fragment_type
Focused-library sequence design: orig, del, or shf (shuffled).
variant_position
Position of the target variant within the fragment: ctr, left, or right.
overlap_hnf1_motif
GSE279071 annotation flag for whether the target variant overlaps an HNF1 motif; NA is retained for controls or missing source flags.
annotation_oligo_type
GSE279071 oligo annotation category, such as tested_var or neg_ctrl.
annotation_match
Whether the S15 fragment matched a GSE279071 annotation record.
alpha_natural_log
Author MPRAnalyze alpha activity estimate on the natural-log scale.
activity_log2
Author Alpha_corrected activity score on the base-2 log scale.
zscore
Author MPRAnalyze Z-score activity statistic.
zscore_pvalue
Nominal author Z-score p-value for activity.
zscore_qvalue_bh_within_promoter
Package Benjamini-Hochberg q-value for the Z-score p-value within the promoter subset.
Package Benjamini-Hochberg q-value for the MAD p-value within the promoter subset.
active_fdr05_zscore
Whether the package Z-score q-value is at most 0.05.
active_fdr05_mad
Whether the package MAD q-value is at most 0.05.
log2_rna_dna_rep1
Author replicate 1 log2 RNA/DNA activity value.
log2_rna_dna_rep2
Author replicate 2 log2 RNA/DNA activity value.
log2_rna_dna_rep3
Author replicate 3 log2 RNA/DNA activity value.
log2_rna_dna_rep4
Author replicate 4 log2 RNA/DNA activity value.
log2_rna_dna_rep5
Author replicate 5 log2 RNA/DNA activity value.
mean_log2_rna_dna_replicates
Mean of the available replicate log2 RNA/DNA activity values.
sd_log2_rna_dna_replicates
Sample standard deviation of the available replicate log2 RNA/DNA activity values.
n_valid_replicates
Number of finite replicate log2 RNA/DNA values used in the mean and standard deviation.
quality_control_pass
All rows in this table passed the package's finite-statistic and replicate-coverage QC.
Quality control
The author/GEO pipeline retained exact barcode-pairing matches, filtered barcode observations using input DNA and RNA-count thresholds, and required at least three of five RNA replicates with nonzero signal before MPRAnalyze modeling; negative controls were used as the activity reference. The package table retains each Table S15 record with finite core MPRAnalyze statistics and at least three finite replicate log2(RNA/DNA) values: 379 of 379 rows passed. The z-score and MAD q-values are package-computed Benjamini-Hochberg adjustments within promoter; they are not presented as author FDR values.
Curation notes
Table S15 is the author-processed result source and includes negative controls as well as motif-focused variant fragments. GSE279071 annotations match every S15 row, but their source metadata contains a stale hg19 assembly note while the annotation file and Table S15 explicitly label the variant coordinates hg38; hg38 is used here. Package q-values are added for discoverability and should not be confused with a reported author FDR.