Experiment / E2ZXDNVHMEpisomal Plasmid MPRA

pMYC QUASARR-seq dual promoter and enhancer library

Dual promoter–enhancer activities reflect a unified regulatory logic

The main QUASARR-seq plasmid library measured intrinsic promoter and enhancer activity for the same candidate human regulatory elements in K-562 cells using paired paBC and eaBC barcode reporters. This table joins the two modality-specific measurements for each element and orientation and includes controls, annotations, and activity calls.

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

Perturbation & assay details

Basal / Untreated

QUASARR-seq is an episomal dual-reporter MPRA. A pMYC minimal promoter drives a luc2 enhancer-activity transcript containing a 3′ eaBC, while the tested TRE drives an egfp promoter-activity transcript containing a 5′ paBC; pA insulators separate the readouts. The library contains candidate promoters, enhancers, inactive controls, positive controls, and variant constructs. Barcode DNA and RNA were sequenced after electroporation into K-562 cells, with two biological replicates and UMI correction; activity statistics are limma/edgeR-derived log2 RNA/DNA effects.

Processed data

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Visible columns (46 of 46)

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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 · 46 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.
promoter_dna_normalized_rep1: Normalized paBC DNA input abundance for promoter replicate 1.
promoter_dna_normalized_rep2: Normalized paBC DNA input abundance for promoter replicate 2.
promoter_rna_normalized_rep1: Normalized paBC RNA abundance for promoter replicate 1.
promoter_rna_normalized_rep2: Normalized paBC RNA abundance for promoter replicate 2.
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 mean negative-control-ORF log2 fold-change for the same orientation.
promoter_activity_call: Source aggregate promoter activity call (active or inactive).
promoter_call_z_score: Orientation-specific promoter activity Z score from the source call analysis.
promoter_call_q_value: Multiple-testing-adjusted Q value from the source promoter activity call analysis.
enhancer_dna_normalized_rep1: Normalized eaBC DNA input abundance for enhancer replicate 1.
enhancer_dna_normalized_rep2: Normalized eaBC DNA input abundance for enhancer replicate 2.
enhancer_rna_normalized_rep1: Normalized eaBC RNA abundance for enhancer replicate 1.
enhancer_rna_normalized_rep2: Normalized eaBC RNA abundance for enhancer replicate 2.
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 mean negative-control-ORF log2 fold-change for the same orientation.
enhancer_activity_call: Source aggregate enhancer activity call (active or inactive).
enhancer_call_z_score: Orientation-specific enhancer activity Z score from the source call analysis.
enhancer_call_q_value: Multiple-testing-adjusted Q value from the source enhancer activity call analysis.
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, limma-voom statistics, and negative-control/orientation-specific activity calls. Package QC retained 1,524 of 1,533 paired element-orientation 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]. Invalid or incomplete rows were excluded; finite nonsignificant rows were retained.

Curation notes

The source workbook and GEO processed tables are the authors' pMYC QUASARR-seq outputs. Coordinates, sequence, GENCODE/PRO-cap annotations, and calls were joined from the Nature Source Data workbook. Variant rows retain the parent/reference sequence because a separate mutant sequence is not supplied. The table retains controls because they are needed to interpret boost indices and call calibration; the separate E0AZJD69U table is the focused variant comparison view.

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