AAV-MPRA 5-bp tiling mutagenesis of chamber-selective enhancers
In Vivo Dissection of Chamber-Selective Enhancers Reveals Estrogen-Related Receptor as a Regulator of Ventricular Cardiomyocyte IdentityA pooled AAV9 library tiled 29 natural 400-bp chamber-selective enhancers with 190-bp WT oligos and matched central 5-bp deletion mutants. The library was assayed in five atrial and four ventricular RNA replicates with five DNA input replicates to identify sequence elements required for chamber activity and selectivity.
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
Basal / untreated; AAV9 mutagenesis library delivered at P0 and heart chambers collected at P7
Each of 29 400-bp enhancers was represented by 80 WT tiles offset by 5 bp, with a paired oligo deleting the central 5 bp. The Methods text calls the WT oligos 190 nt, while the Figure 5 caption and deposited coordinate spans describe 180-bp oligos; the package preserves the deposited coordinates. Each oligo carried a unique 10-nt barcode. The library also contained negative ESC-derived controls and positive enhancer controls. GEO supplies deduplicated read counts for five DNA, five atrial RNA, and four ventricular RNA samples.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (75 of 75)
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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 · 75 definitions
- oligo_id
- Exact deposited mutagenesis-library region identifier.
- parent_enhancer_region
- 400-bp parent region for tiling enhancers or the source control interval.
- design_id
- Source design token or control name.
- library_class
- Source library class: A_enhancers, V_enhancers, AV_enhancers, enhancer positive controls, or ESC_enhancers.
- source_region_id
- Source genomic region used to identify the parent enhancer or control.
- oligo_interval
- 180-bp oligo interval reported by the source.
- tile_index
- Source 5-bp tile index; 1–80 for the 400-bp tiling library and a source control token for controls.
- tile_start_offset_bp
- Approximate 0-based offset of the tile within the parent region, calculated as (tile index minus 1) × 5 when the tile index is 1–80.
- oligo_type
- WT wild-type tile or Mut tile with the central 5 bp deleted.
- sequence_5mer
- Deposited 5-bp sequence for WT rows; the source token NO for Mut rows.
- wildtype_sequence_5mer
- Wild-type 5-bp sequence for the row’s WT–Mut pair, when available.
- deleted_5bp
- 5-bp sequence deleted in the paired Mut oligo; blank for WT/control rows.
- pair_id
- Stable identifier for a WT–Mut oligo pair; control-only rows receive a stable singleton identifier.
- pair_complete
- TRUE when both WT and Mut members passed the DNA-coverage filter.
- chromosome
- Chromosome parsed from the parent enhancer/control coordinate.
- enhancer_start
- Parent region start coordinate.
- enhancer_end
- Parent region end coordinate.
- enhancer_length_bp
- Parent coordinate span calculated as end minus start.
- dna_count_rep1
- Deposited DNA read count for replicate 1.
- dna_count_rep2
- Deposited DNA read count for replicate 2.
- dna_count_rep3
- Deposited DNA read count for replicate 3.
- dna_count_rep4
- Deposited DNA read count for replicate 4.
- dna_count_rep5
- Deposited DNA read count for replicate 5.
- atrium_rna_count_rep1
- Deposited atrial RNA read count for replicate 1.
- atrium_rna_count_rep2
- Deposited atrial RNA read count for replicate 2.
- atrium_rna_count_rep3
- Deposited atrial RNA read count for replicate 3.
- atrium_rna_count_rep4
- Deposited atrial RNA read count for replicate 4.
- atrium_rna_count_rep5
- Deposited atrial RNA read count for replicate 5.
- ventricle_rna_count_rep1
- Deposited ventricular RNA read count for replicate 1.
- ventricle_rna_count_rep2
- Deposited ventricular RNA read count for replicate 2.
- ventricle_rna_count_rep3
- Deposited ventricular RNA read count for replicate 3.
- ventricle_rna_count_rep4
- Deposited ventricular RNA read count for replicate 4.
- dna_fpm_rep1
- DNA replicate 1 read count normalized to fragments per million within that sample.
- dna_fpm_rep2
- DNA replicate 2 read count normalized to fragments per million within that sample.
- dna_fpm_rep3
- DNA replicate 3 read count normalized to fragments per million within that sample.
- dna_fpm_rep4
- DNA replicate 4 read count normalized to fragments per million within that sample.
- dna_fpm_rep5
- DNA replicate 5 read count normalized to fragments per million within that sample.
- atrium_rna_fpm_rep1
- atrial RNA replicate 1 read count normalized to fragments per million within that sample.
- atrium_rna_fpm_rep2
- atrial RNA replicate 2 read count normalized to fragments per million within that sample.
- atrium_rna_fpm_rep3
- atrial RNA replicate 3 read count normalized to fragments per million within that sample.
- atrium_rna_fpm_rep4
- atrial RNA replicate 4 read count normalized to fragments per million within that sample.
- atrium_rna_fpm_rep5
- atrial RNA replicate 5 read count normalized to fragments per million within that sample.
- ventricle_rna_fpm_rep1
- ventricular RNA replicate 1 read count normalized to fragments per million within that sample.
- ventricle_rna_fpm_rep2
- ventricular RNA replicate 2 read count normalized to fragments per million within that sample.
- ventricle_rna_fpm_rep3
- ventricular RNA replicate 3 read count normalized to fragments per million within that sample.
- ventricle_rna_fpm_rep4
- ventricular RNA replicate 4 read count normalized to fragments per million within that sample.
- dna_fpm_mean
- Mean DNA fragments per million across five DNA replicates.
- dna_fpm_max
- Maximum DNA fragments per million across five DNA replicates; individual-oligo QC requires ≥5.
- atrium_rna_fpm_mean
- Mean atrial RNA fragments per million across five replicates.
- ventricle_rna_fpm_mean
- Mean ventricular RNA fragments per million across four replicates.
- atrium_activity_log2
- Mean per-replicate log2((atrial RNA FPM + 0.5)/(DNA FPM + 0.5)).
- ventricle_activity_log2
- Mean per-replicate log2((ventricular RNA FPM + 0.5)/(DNA FPM + 0.5)).
- atrium_vs_ventricle_log2
- Atrial activity log2 score minus ventricular activity log2 score.
- atrium_vs_ventricle_ratio
- Two raised to atrium_vs_ventricle_log2; values above 1 favor atrial activity.
- atrium_activity_p_value
- Two-sided one-sample t-test p-value for atrial activity scores versus zero.
- ventricle_activity_p_value
- Two-sided one-sample t-test p-value for ventricular activity scores versus zero.
- atrium_active_nominal
- Nominal activity flag using a positive score and unadjusted p<0.05; not the paper’s motif-call criterion.
- ventricle_active_nominal
- Nominal activity flag using a positive score and unadjusted p<0.05; not the paper’s motif-call criterion.
- paired_wt_activity_atrium_log2
- Atrial activity score of the WT member of the complete pair.
- paired_mut_activity_atrium_log2
- Atrial activity score of the Mut member of the complete pair.
- paired_mut_minus_wt_atrium_log2
- Mut minus WT atrial activity log2 score.
- paired_mut_minus_wt_atrium_p_value
- Two-sided one-sample t-test p-value for per-replicate Mut minus WT atrial activity differences.
- paired_mut_minus_wt_atrium_fdr
- Benjamini-Hochberg FDR across complete-pair atrial effects.
- paired_wt_activity_ventricle_log2
- Ventricular activity score of the WT member of the complete pair.
- paired_mut_activity_ventricle_log2
- Ventricular activity score of the Mut member of the complete pair.
- paired_mut_minus_wt_ventricle_log2
- Mut minus WT ventricular activity log2 score.
- paired_mut_minus_wt_ventricle_p_value
- Two-sided one-sample t-test p-value for per-replicate Mut minus WT ventricular activity differences.
- paired_mut_minus_wt_ventricle_fdr
- Benjamini-Hochberg FDR across complete-pair ventricular effects.
- paired_wt_selectivity_log2
- WT atrial-minus-ventricular activity log2 score.
- paired_mut_selectivity_log2
- Mut atrial-minus-ventricular activity log2 score.
- paired_mut_minus_wt_selectivity_log2
- Change in chamber selectivity caused by the 5-bp deletion: Mut selectivity minus WT selectivity.
- paired_atrium_effect_significant_fdr_0_05
- TRUE when the paired atrial deletion effect has FDR<0.05.
- paired_ventricle_effect_significant_fdr_0_05
- TRUE when the paired ventricular deletion effect has FDR<0.05.
- qc_individual_dna_pass
- TRUE when at least one DNA replicate has ≥5 FPM before pair-completeness filtering.
- qc_pass
- TRUE for every retained row; low-coverage oligos and unpaired low-coverage Mut rows are excluded.
Quality control
The article explicitly excludes oligos with <5 FPM DNA coverage. The package applies the matching max-across-five-DNA-replicates ≥5 FPM gate, retains all passing WT oligos, and retains a Mut oligo only when its matching WT also passes, so the complete paired set is directly interpretable. This yields 2,394 WT rows and 1,761 complete WT–Mut pairs, matching the paper; rows are excluded before table.csv generation if they fail the individual or pair-completeness gate. Paired deletion effects are calculated from replicate-level log2 RNA/DNA differences and BH-adjusted across complete pairs.
Curation notes
AAV9 libraries were delivered systemically to P0 mouse pups and atria and ventricles were collected at P7. The combined biosample is represented as UNMAPPED because the same library was read out in two distinct primary cardiomyocyte populations; the constituent Cell Ontology terms are CL:0002129 (regular atrial cardiac myocyte) and CL:0002131 (regular ventricular cardiac myocyte). The deposited table contains 5,066 oligo rows, including 29 tiling enhancers plus ESC negative controls and positive enhancer controls. After the coverage and pair-completeness filters, table.csv contains 4,155 rows: 2,394 WT rows and one Mut row for each of 1,761 complete pairs. There is a source-length discrepancy: the Methods text says 190-nt oligos, but the Figure 5 caption and GEO coordinate spans use 180 bp; this package retains the GEO coordinates and does not infer unreported sequence bases. Mutagenesis count tables do not include the full WT or mutant sequence; only the WT 5-mer and deleted 5-bp token are available, so full mutant sequences are not inferred. The article’s motif-enrichment analysis is not recomputed; pair-level activity effects are provided as a reusable quantitative summary.