Experiment / E3PLSKS7GEpisomal Plasmid MPRA

R1-MPRA: iterative MPRA-designed synthetic enhancers

Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity

A 145-bp synthetic enhancer library designed with MPRA-trained neural-network models and tested in HepG2 and K562 cells. The table combines GEO DNA/RNA counts, derived RNA/DNA activity, and the authors’ design and DESeq2 annotations.

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:0027;CVCL:0004
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / untreated cell culture

Enhancer sequences were cloned upstream of a minimal promoter and reporter with multiple 3-prime UTR barcodes; reporter RNA and plasmid DNA were sequenced after transfection.

Processed data

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

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Visible columns (43 of 43)

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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 · 43 definitions

element_id: Unique identifier for the tested enhancer element.
enhancer_sequence: DNA sequence assayed as the reporter enhancer.
sequence_length_bp: Length of the tested enhancer sequence in base pairs.
barcode_sequences: Semicolon-separated reporter barcode sequences associated with the element.
barcode_count: Number of barcodes associated with the element.
design_target_cell_type: Design target cell type.
design_model: Design model.
design_generator: Design generator.
design_model_type: Design model type.
dataset_split: Dataset split.
model_predicted_log2_H2K: Model-predicted HepG2-versus-K562 differential activity.
motif_count: Motif count.
unique_motif_clusters: Unique motif clusters.
dna_count: DNA plasmid abundance count from the MPRA library.
hepg2_rna_rep1_count: Hepg2 rna rep1 count.
hepg2_rna_rep2_count: Hepg2 rna rep2 count.
k562_rna_rep1_count: K562 rna rep1 count.
k562_rna_rep2_count: K562 rna rep2 count.
hepg2_log2_rna_dna_rep1: Hepg2 log2 rna dna rep1.
hepg2_log2_rna_dna_rep2: Hepg2 log2 rna dna rep2.
hepg2_log2_rna_dna_mean: Hepg2 log2 rna dna mean.
hepg2_log2_rna_dna_sd: Hepg2 log2 rna dna sd.
k562_log2_rna_dna_rep1: K562 log2 rna dna rep1.
k562_log2_rna_dna_rep2: K562 log2 rna dna rep2.
k562_log2_rna_dna_mean: K562 log2 rna dna mean.
k562_log2_rna_dna_sd: K562 log2 rna dna sd.
derived_log2_rna_dna_H2K: Derived HepG2-minus-K562 differential activity from the processed counts.
author_baseMean_HepG2: Author basemean hepg2.
author_log2FoldChange_HepG2: Author log2foldchange hepg2.
author_lfcSE_HepG2: Author lfcse hepg2.
author_pvalue_HepG2: Author pvalue hepg2.
author_padj_HepG2: Author padj hepg2.
author_baseMean_K562: Author basemean k562.
author_log2FoldChange_K562: Author log2foldchange k562.
author_lfcSE_K562: Author lfcse k562.
author_pvalue_K562: Author pvalue k562.
author_padj_K562: Author padj k562.
author_log2FoldChange_H2K: Authors’ DESeq2 HepG2-versus-K562 log2 fold-change or differential activity statistic.
author_log2FoldChange_H2K_cell_difference: Author log2foldchange h2k cell difference.
author_lfcSE_H2K: Author lfcse h2k.
author_padj_H2K: Authors’ multiple-testing-adjusted p-value for the HepG2-versus-K562 contrast.
author_processed_stats_available: Author processed stats available.
qc_pass: Pass/fail flag for sequence, barcode, DNA-count, and RNA-count quality checks.

Quality control

Retained source rows with valid nonempty ACGT sequence, positive DNA count, nonnegative RNA counts, and at least one barcode. All 1346/1346 R1-MPRA rows passed these checks.

Curation notes

The authors report 1,037 designed sequences plus controls in the R1-MPRA library; the deposited processed count table contains 1,346 element rows including controls and associated designs.

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