WTC11 enhancer perturbation e2MPRA library
Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRAA 100-bp enhancer perturbation library in WTC11 human iPSCs tested single-nucleotide substitutions and two randomized 6-bp sliding-window perturbations per position across selected pluripotency-associated CREs, with integrated lentiMPRA and targeted ATAC-seq/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.
WTC11 iPSCs were transduced with an integrated lentiviral 100-bp CRE library carrying random 15-bp barcodes. Each selected active CRE was tested with all three alternate nucleotides at every position and with two independent 6-bp sliding-window randomizations; lentiMPRA, targeted ATAC-seq, and H3K27ac CUT&Tag were measured in three replicate assays.
Processed data
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Visible columns (62 of 62)
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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, parent, perturbation, or calibration-control category assigned from the library design.
- template
- Synthetic template label when applicable; blank for this WTC11 library.
- tf_motifs
- Semicolon-separated transcription-factor motif names represented in a synthetic design; blank for this WTC11 library.
- motif_order
- Order of motifs in a synthetic construct; blank for this WTC11 library.
- motif_counts
- Per-motif copy numbers in a synthetic construct; blank for this WTC11 library.
- parent_cre
- Wild-type parent CRE for a perturbed construct.
- variant_type
- Single-nucleotide substitution or 6-bp sliding-window randomization.
- variant_position
- One-based position of a single-nucleotide substitution.
- reference_allele
- Reference allele encoded in a single-nucleotide variant identifier; the sequence column contains the mutated construct.
- alternate_allele
- Alternate allele encoded in a single-nucleotide 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 the indicated single-nucleotide substitution.
- published_lentiMPRA_variant_neglog10_p
- Published -log10(p) for the lentiMPRA variant-effect coefficient.
- published_ATAC_variant_effect
- Published ATAC linear-regression coefficient for the indicated single-nucleotide substitution.
- published_ATAC_variant_neglog10_p
- Published -log10(p) for the ATAC variant-effect coefficient.
- published_H3K27ac_variant_effect
- Published H3K27ac linear-regression coefficient for the indicated single-nucleotide substitution.
- published_H3K27ac_variant_neglog10_p
- Published -log10(p) for the H3K27ac variant-effect coefficient.
- 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. One active CRE (seq6846_R) and its variants were excluded for insufficient read coverage, and the four inactive experimental CREs were excluded from downstream analyses because their MPRA activity was too weak. The processed table includes the four analyzed active CREs, passing perturbations, and passing calibration controls, requiring complete three-replicate lentiMPRA measurements with positive counts, at least 5 observed barcodes per replicate, and positive gDNA insertion counts; this yields 2,160 rows.
Curation notes
WTC11 is a named human iPSC line; CL:0002248 is the general Cell Ontology pluripotent-stem-cell mapping used here. The table includes the four analyzed active CREs (seq68781_R, seq5934_F, POU5F1_DE_core, NANOG_p), their passing SNV and 6-bp-window constructs, and passing calibration controls. seq6846_R, all four inactive experimental CREs, and the four constructs lacking sufficient lentiMPRA/source coverage are excluded. Variant coefficients from Source Data Fig. 5 and Fig. S7 are widened into lentiMPRA, ATAC, and H3K27ac columns; source blanks are not imputed.