HepG2 synthetic enhancer e2MPRA library
Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRAA synthetic enhancer library arranged nine liver-expressed TF motifs in three combinatorial classes on two neutral templates, with 200 pilot-derived controls, and assayed it in HepG2 cells by integrated lentiMPRA plus targeted ATAC-seq and H3K27ac CUT&Tag.
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
Perturbation not reported.
The library placed CEBPA, CTCF, FOXA1, HNF1A, NR2F2, ONECUT1, PPARA, REST, and XBP1 motifs in homotypic, two-TF, and four-TF arrangements on two neutral 100-bp templates. Three independent library infections were assayed by lentiMPRA, targeted ATAC-seq, and H3K27ac CUT&Tag; the two templates were treated as biological design replicates for the synthetic sequences.
Processed data
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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 · 62 definitions
- element_id
- Unique sequence identifier from the deposited library design.
- sequence
- Designed reporter sequence.
- sequence_length
- Sequence length in nucleotides.
- library_feature
- Numeric library feature identifier from the deposited lentiMPRA count table.
- element_category
- Functional or control category assigned from the library design.
- template
- Synthetic template label when applicable; blank for other elements.
- tf_motifs
- Semicolon-separated transcription-factor motif names represented in a synthetic design.
- motif_order
- Order of motifs in a synthetic construct, with > separating positions.
- motif_counts
- Per-motif copy numbers encoded as TF:count pairs separated by semicolons.
- parent_cre
- Wild-type parent CRE for a perturbed construct; blank for this synthetic library.
- variant_type
- Type of sequence perturbation; blank for non-variant elements.
- variant_position
- One-based position of a single-nucleotide substitution.
- reference_allele
- Reference allele encoded in a variant identifier.
- alternate_allele
- Alternate allele encoded in a variant identifier.
- window_start
- One-based start of a randomized sliding window.
- window_end
- One-based end of a randomized sliding window.
- window_randomization_rep
- Independent randomization number for a window perturbation.
- dna_count_rep1
- Deposited lentiMPRA DNA count summary for replicate 1.
- dna_count_rep2
- Deposited lentiMPRA DNA count summary for replicate 2.
- dna_count_rep3
- Deposited lentiMPRA DNA count summary for replicate 3.
- rna_count_rep1
- Deposited lentiMPRA RNA count summary for replicate 1.
- rna_count_rep2
- Deposited lentiMPRA RNA count summary for replicate 2.
- rna_count_rep3
- Deposited lentiMPRA RNA count summary for replicate 3.
- observed_barcode_count_rep1
- Number of element barcodes observed in the filtered DNA/RNA barcode set for replicate 1.
- observed_barcode_count_rep2
- Number of element barcodes observed in the filtered DNA/RNA barcode set for replicate 2.
- observed_barcode_count_rep3
- Number of element barcodes observed in the filtered DNA/RNA barcode set for replicate 3.
- lentiMPRA_log2_rna_dna_raw_rep1
- Log2 of the deposited RNA/DNA count ratio before the paper's TMM normalization, replicate 1.
- lentiMPRA_log2_rna_dna_raw_rep2
- Log2 of the deposited RNA/DNA count ratio before the paper's TMM normalization, replicate 2.
- lentiMPRA_log2_rna_dna_raw_rep3
- Log2 of the deposited RNA/DNA count ratio before the paper's TMM normalization, replicate 3.
- lentiMPRA_log2_activity_rep1
- Published TMM-normalized log2 lentiMPRA activity for replicate 1.
- lentiMPRA_log2_activity_rep2
- Published TMM-normalized log2 lentiMPRA activity for replicate 2.
- lentiMPRA_log2_activity_rep3
- Published TMM-normalized log2 lentiMPRA activity for replicate 3.
- gDNA_count_rep1
- e2MPRA genomic-DNA insertion count for replicate 1.
- gDNA_count_rep2
- e2MPRA genomic-DNA insertion count for replicate 2.
- gDNA_count_rep3
- e2MPRA genomic-DNA insertion count for replicate 3.
- ATAC_count_rep1
- e2MPRA targeted ATAC-seq enriched count for replicate 1.
- ATAC_count_rep2
- e2MPRA targeted ATAC-seq enriched count for replicate 2.
- ATAC_count_rep3
- e2MPRA targeted ATAC-seq enriched count for replicate 3.
- H3K27ac_count_rep1
- e2MPRA H3K27ac CUT&Tag enriched count for replicate 1.
- H3K27ac_count_rep2
- e2MPRA H3K27ac CUT&Tag enriched count for replicate 2.
- H3K27ac_count_rep3
- e2MPRA H3K27ac CUT&Tag enriched count for replicate 3.
- ATAC_log2_activity_rep1
- Published TMM-normalized log2 ATAC enrichment relative to gDNA for replicate 1.
- ATAC_log2_activity_rep2
- Published TMM-normalized log2 ATAC enrichment relative to gDNA for replicate 2.
- ATAC_log2_activity_rep3
- Published TMM-normalized log2 ATAC enrichment relative to gDNA for replicate 3.
- H3K27ac_log2_activity_rep1
- Published TMM-normalized log2 H3K27ac enrichment relative to gDNA for replicate 1.
- H3K27ac_log2_activity_rep2
- Published TMM-normalized log2 H3K27ac enrichment relative to gDNA for replicate 2.
- H3K27ac_log2_activity_rep3
- Published TMM-normalized log2 H3K27ac enrichment relative to gDNA for replicate 3.
- lentiMPRA_log2_activity_mean_replicates
- Arithmetic mean of available published lentiMPRA replicate activity scores.
- ATAC_log2_activity_mean_replicates
- Arithmetic mean of available published ATAC replicate activity scores.
- H3K27ac_log2_activity_mean_replicates
- Arithmetic mean of available published H3K27ac replicate activity scores.
- lentiMPRA_log2_activity_published
- Published aggregate TMM-normalized lentiMPRA log2 activity from Source Data Fig. 2; blank for this library.
- ATAC_log2_activity_published
- Published aggregate TMM-normalized ATAC log2 activity from Source Data Fig. 2; blank for this library.
- H3K27ac_log2_activity_published
- Published aggregate TMM-normalized H3K27ac log2 activity from Source Data Fig. 2; blank for this library.
- published_lentiMPRA_variant_effect
- Published lentiMPRA linear-regression coefficient for a single-nucleotide variant; blank for this library.
- published_lentiMPRA_variant_neglog10_p
- Published -log10(p) for the lentiMPRA variant-effect coefficient; blank for this library.
- published_ATAC_variant_effect
- Published ATAC variant-effect coefficient; blank for this library.
- published_ATAC_variant_neglog10_p
- Published -log10(p) for the ATAC variant-effect coefficient; blank for this library.
- published_H3K27ac_variant_effect
- Published H3K27ac variant-effect coefficient; blank for this library.
- published_H3K27ac_variant_neglog10_p
- Published -log10(p) for the H3K27ac variant-effect coefficient; blank for this library.
- total_gDNA_count
- Sum of gDNA insertion counts across the three replicates.
- total_ATAC_count
- Sum of targeted ATAC-seq enriched counts across the three replicates.
- total_H3K27ac_count
- Sum of H3K27ac CUT&Tag enriched counts across the three replicates.
Quality control
The paper retained barcodes observed in both DNA and RNA within each replicate and excluded elements with fewer than 5 unique barcodes; TMM normalization used 200 control sequences. All sequences containing the NR2F2 motif were excluded because they had absent or very low genomic counts. The processed table further requires complete three-replicate lentiMPRA measurements with positive counts and complete positive-gDNA e2MPRA insertion measurements, yielding 3,833 rows; DNasePeakNoPromoter_41 is absent from the lentiMPRA data and is therefore not included.
Curation notes
The two neutral template references and all non-NR2F2 synthetic constructs are represented with their designed sequences and motif annotations. The table includes the 200 controls because they are useful calibration elements even though the paper used them only for TMM normalization. Nineteen retained elements have blank published per-replicate ATAC/H3K27ac activity values while retaining complete deposited raw counts.