Experiment / E7XWTIBYAEpisomal Plasmid MPRA

QUASARR-seq minimal-promoter comparison

Dual promoter–enhancer activities reflect a unified regulatory logic

A matched QUASARR-seq library tested the same TRE collection with pGAPDH, pMYC, and pAPOBEC3F minimal promoters to measure how promoter context modulates enhancer and promoter readouts. The table is in long format, with one row per element, orientation, and minimal-promoter context.

Download processed table (CSV)Raw source data API documentation

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:0004
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

This is the QUASARR-seq dual-reporter configuration with three minimal-promoter contexts (pGAPDH, pMYC, and pAPOBEC3F). Each context has paired eaBC enhancer and paBC promoter measurements from two biological replicates after K-562 electroporation. DNA/RNA barcode abundance, limma statistics, and context-specific negative-control-normalized boost indices are provided.

Processed data

50 rows per page. Click a cell to inspect its full value.

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Visible columns (41 of 41)

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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 · 41 definitions

element_id: Unique source element identifier including strand orientation.
base_element_id: Orientation-free source element identifier.
orientation: Element orientation in the reporter construct (fwd or rev).
construct_type: Package classification of the source construct, such as candidate_TRE, variant, control, or positive_control.
mutation: Allele or mutation notation from the source mutation annotation; blank for non-variant constructs.
mutation_category: Source mutation category; blank for non-variant constructs.
chromosome: GRCh38 chromosome for the annotated genomic element.
start: GRCh38 start coordinate of the annotated element.
end: GRCh38 end coordinate of the annotated element.
reference_sequence: Reference or parent sequence used for the construct.
sequence_length: Reference sequence length in base pairs.
gc_content_percent: GC percentage calculated from reference_sequence.
gencode_distance_class: Source GENCODE proximity class (for example, Proximal or Distal).
procap_class: Source PRO-cap transcription class (Transcribed or Untranscribed where available).
protein_coding_status: Source annotation indicating overlap with protein-coding GENCODE elements.
lncRNA_status: Source annotation indicating overlap with lncRNA GENCODE elements.
procap_count: Source PRO-cap signal/count for the element.
min_promoter: Minimal-promoter context used in the QUASARR-seq construct (pGAPDH, pMYC, or pAPOBEC3F).
promoter_dna_normalized_rep1: Normalized paBC DNA input abundance for promoter replicate 1 in this minimal-promoter context.
promoter_dna_normalized_rep2: Normalized paBC DNA input abundance for promoter replicate 2 in this minimal-promoter context.
promoter_rna_normalized_rep1: Normalized paBC RNA abundance for promoter replicate 1 in this minimal-promoter context.
promoter_rna_normalized_rep2: Normalized paBC RNA abundance for promoter replicate 2 in this minimal-promoter context.
promoter_log2_fold_change: Limma log2 fold-change activity estimate for promoter paBC RNA relative to DNA input.
promoter_average_expression: Limma average-expression statistic for the promoter measurement.
promoter_t_statistic: Moderated limma t statistic for promoter activity.
promoter_p_value: Raw limma P value for promoter activity.
promoter_fdr: Benjamini-Hochberg adjusted limma P value for promoter activity.
promoter_log_odds: Limma B statistic (log-odds of differential activity) for promoter activity.
promoter_boost_index: Promoter log2 fold-change minus the context-specific mean negative-control-ORF log2 fold-change.
enhancer_dna_normalized_rep1: Normalized eaBC DNA input abundance for enhancer replicate 1 in this minimal-promoter context.
enhancer_dna_normalized_rep2: Normalized eaBC DNA input abundance for enhancer replicate 2 in this minimal-promoter context.
enhancer_rna_normalized_rep1: Normalized eaBC RNA abundance for enhancer replicate 1 in this minimal-promoter context.
enhancer_rna_normalized_rep2: Normalized eaBC RNA abundance for enhancer replicate 2 in this minimal-promoter context.
enhancer_log2_fold_change: Limma log2 fold-change activity estimate for enhancer eaBC RNA relative to DNA input.
enhancer_average_expression: Limma average-expression statistic for the enhancer measurement.
enhancer_t_statistic: Moderated limma t statistic for enhancer activity.
enhancer_p_value: Raw limma P value for enhancer activity.
enhancer_fdr: Benjamini-Hochberg adjusted limma P value for enhancer activity.
enhancer_log_odds: Limma B statistic (log-odds of differential activity) for enhancer activity.
enhancer_boost_index: Enhancer log2 fold-change minus the context-specific mean negative-control-ORF log2 fold-change.
source_data: Provenance of the joined measurements and annotations.

Quality control

The authors used fastp preprocessing, barcode clustering at Hamming distance 1, partial-element alignment, UMI correction, edgeR modeling, TMM normalization against negative-control ORFs, and limma-voom statistics. Package QC retained 8,274 of the paired element-orientation-context rows after requiring matching promoter and enhancer records, finite normalized DNA/RNA values and limma logFC/AveExpr/t/P.Value/adj.P.Val/B statistics, positive normalized DNA/RNA values, and P.Value and adj.P.Val in [0,1]. Rows with incomplete or invalid measurements were excluded; finite nonsignificant rows were retained. Retained rows comprise pGAPDH (3,039), pMYC (2,553), and pAPOBEC3F (2,682) contexts.

Curation notes

Rows are intentionally long-format so the three minimal-promoter contexts can be compared without conflating their distinct normalizations. Context-specific boost indices were calculated using the mean negative-control-ORF log2 fold-change for that context. Source data are the Nature workbook sheets and matching GEO processed limma tables.

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