PPIF promoter lentiMPRA in THP-1 cells
Rewriting regulatory DNA to dissect and reprogram gene expressionA 250-bp hg19 PPIF promoter oligo library spanning -200 to +50 bp relative to the transcription start site, including the wild-type promoter, dinucleotide shuffles, controls, and 353 designed promoter variants, was cloned into the pLS-SceI lentiMPRA vector. The library was assayed in three biological replicates in THP-1 cells, with reporter RNA/DNA barcode ratios and mpralm comparisons to the wild-type promoter used to quantify variant effects.
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
PPIF promoter oligos spanning hg19 chr10:81107018-81107268 (-200 to +50 bp relative to the TSS) were cloned into the pLS-SceI lentiMPRA vector. Each oligo was associated with a 15-bp random barcode; THP-1 cells were infected at MOI 30, and RNA and DNA barcode libraries were sequenced for three biological replicates. A 10-bp UMI was used to remove PCR duplicates, and mpralm differential analysis compared each promoter variant with the PPIF promoter wild-type 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 · 24 definitions
- variant_id
- Study variant identifier in chr:position:reference>alternate format.
- chromosome
- Chromosome containing the PPIF promoter variant.
- position_1based
- 1-based leftmost genomic position of the variant.
- ref_allele
- Reference sequence replaced by the designed promoter oligo allele.
- alt_allele
- Alternate sequence in the designed promoter oligo.
- ref_end_1based
- 1-based inclusive end coordinate of the reference sequence.
- variant_class
- Sequence-length class: substitution, insertion, deletion, or replacement.
- mapped_barcode_count
- Number of barcode-to-element mapping records for the variant in CRS-BC analysis.
- n_biological_replicates
- Number of biological replicates represented in the reporter-level output.
- min_observed_barcodes
- Minimum observed barcode count across the three biological replicates.
- mean_dna_counts
- Mean unnormalized DNA barcode counts across biological replicates.
- mean_rna_counts
- Mean unnormalized RNA barcode counts across biological replicates.
- mean_dna_normalized_cpm
- Mean DNA barcode counts normalized as reported by MPRAsnakeflow, across replicates.
- mean_rna_normalized_cpm
- Mean RNA barcode counts normalized as reported by MPRAsnakeflow, across replicates.
- mean_rna_dna_ratio
- Mean RNA-to-DNA reporter ratio across biological replicates.
- mean_log2_activity
- Mean log2 RNA/DNA reporter activity across biological replicates.
- sd_log2_activity
- Sample standard deviation of log2 RNA/DNA reporter activity across replicates.
- log2_fc_vs_WT
- mpralm log2 fold-change in reporter expression versus the PPIF promoter wild-type oligo.
- average_expression
- mpralm average expression value (AveExpr).
- t_statistic
- mpralm moderated t-statistic for the variant-versus-wild-type contrast.
- p_value
- Raw mpralm p-value for the variant-versus-wild-type contrast.
- adjusted_p_value
- Benjamini-Hochberg adjusted mpralm p-value.
- b_statistic
- mpralm B-statistic, the log-odds measure of differential reporter activity.
- significant_fdr_0_05
- TRUE when the adjusted mpralm p-value is at most 0.05; otherwise FALSE.
Quality control
The study's MPRAsnakeflow/mpralm workflow filtered ambiguous or incorrectly sized 15-bp barcode and 10-bp UMI reads, counted each barcode-UMI pair once to remove PCR duplicates, removed barcodes with zero RNA or DNA counts, and retained oligos with at least 10 observed barcodes. For this packaged table, variants were additionally required to have records in all 3 biological replicates, positive RNA and DNA counts in every replicate, at least 10 observed barcodes in every replicate, and a barcode-to-element mapping. All 353 mpralm variants passed these filters; the minimum observed barcode count among retained variants was 14.
Curation notes
The publication primarily reports endogenous Variant-EFFECTS screens using prime editing and RNA FlowFISH; this package contains only its separate PPIF promoter lentiMPRA comparison. The processed table is restricted to the 353 chr10 PPIF promoter variants represented in the mpralm results, excluding control constructs and the unrelated genomic control interval present in the MPRAsnakeflow output. IGVFDS1282YUKL is the original mpralm accession and is documented by the portal as merged into IGVFDS1376WOXJ; metadata snapshots for the relevant portal analyses are retained in raw_data.