Experiment / E912XLYZLEpisomal Plasmid MPRA

R2 MPRA: iteratively retrained synthetic enhancer library

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

A second-generation library of synthetic enhancer sequences generated after retraining on R1 measurements, including full-length and truncation/perturbation designs. The table contains all deposited R2 count rows with derived cell-type activity and repository annotations where a key match exists.

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

Enhancers were assayed in the same plasmid reporter configuration in HepG2 and K562; the library includes 145-, 72-, 50-, and 25-bp designs and two barcodes per element.

Processed data

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

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Visible columns (37 of 37)

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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 · 37 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_type: Design type.
design_model_type: Design model type.
design_target_log2_H2K: Design target log2 h2k.
model_predicted_log2_HepG2: Model predicted log2 hepg2.
model_predicted_log2_K562: Model predicted log2 k562.
model_predicted_log2_H2K: Model-predicted HepG2-versus-K562 differential activity.
motif_count: Motif count.
unique_motif_clusters: Unique motif clusters.
dna_rep1_count: DNA plasmid abundance count from R2 DNA replicate 1.
dna_rep2_count: DNA plasmid abundance count from R2 DNA replicate 2.
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_log2FoldChange_HepG2: Author log2foldchange hepg2.
author_lfcSE_HepG2: Author lfcse hepg2.
author_log2FoldChange_K562: Author log2foldchange k562.
author_lfcSE_K562: Author lfcse k562.
author_log2FoldChange_H2K: Authors’ DESeq2 HepG2-versus-K562 log2 fold-change or differential activity statistic.
author_lfcSE_H2K: Author lfcse h2k.
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 counts in both DNA replicates, nonnegative RNA counts, and exactly two barcodes. All 1802/1802 R2 rows passed these checks.

Curation notes

The repository d3 annotation table covers 1,729 rows. Seventy-three valid 145-bp GEO count rows lacked a repository annotation key and are retained with null author/model fields and generated R2_unannotated element IDs.

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