HepG2 pilot e2MPRA library
Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRAA 400-element pilot library of 100-bp genomic and synthetic CREs was assayed in HepG2 cells using integrated lentiMPRA, with targeted ATAC-seq and H3K27ac CUT&Tag measurements on the same integrated library.
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.
Lentivirus integrated a 400-element, 100-bp CRE library carrying random 15-bp barcodes into HepG2 cells at an estimated MOI of 50. Three independent replicate assays measured lentiMPRA RNA/DNA activity, targeted ATAC-seq accessibility, and H3K27ac CUT&Tag enrichment.
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 the pilot 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; populated for the pilot library.
- ATAC_log2_activity_published
- Published aggregate TMM-normalized ATAC log2 activity from Source Data Fig. 2; populated for the pilot library.
- H3K27ac_log2_activity_published
- Published aggregate TMM-normalized H3K27ac log2 activity from Source Data Fig. 2; populated for the pilot library.
- published_lentiMPRA_variant_effect
- Published lentiMPRA linear-regression coefficient for a single-nucleotide variant; blank in this pilot experiment.
- published_lentiMPRA_variant_neglog10_p
- Published -log10(p) for the lentiMPRA variant-effect coefficient; blank in this pilot experiment.
- published_ATAC_variant_effect
- Published ATAC variant-effect coefficient; blank in this pilot experiment.
- published_ATAC_variant_neglog10_p
- Published -log10(p) for the ATAC variant-effect coefficient; blank in this pilot experiment.
- published_H3K27ac_variant_effect
- Published H3K27ac variant-effect coefficient; blank in this pilot experiment.
- published_H3K27ac_variant_neglog10_p
- Published -log10(p) for the H3K27ac variant-effect coefficient; blank in this pilot experiment.
- 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; replicate and assay values were TMM-normalized using random genomic controls. The processed table retains the 399 pilot elements with complete three-replicate lentiMPRA measurements and excludes DNasePeakNoPromoter_41, the single design without lentiMPRA coverage. Blank published e2MPRA activity values were not treated as failed QC when the deposited gDNA, ATAC, and H3K27ac counts were present.
Curation notes
The pilot e2MPRA count block was taken from Source Data FigS2. The similarly named supplementary sheet is a duplicate of the HepG2 synthetic-library e2 counts, so it was not used for the pilot epigenomic counts. All retained rows have positive DNA/RNA counts and at least five observed barcodes in each lentiMPRA replicate; e2 activity scores are left blank where the published per-replicate source value is blank.