Dynamic P300 enhancer regions across cardiomyocyte maturation
Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturationAn in vivo AAV9 MPRA tested 400-bp mouse genomic regions centered on dynamic Early and Late P300 regions, together with static, positive-control, and negative-control elements. The library was delivered to E15.5 embryos for P0 collection or to P0 pups for P7 and P28 collection, and enhancer activity was measured from ventricular mCherry RNA relative to AAV DNA.
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 / developmental time course: E15.5 embryo injection with P0 collection, or P0 pup injection with P7/P28 collection
Self-complementary AAV9 episomal reporter with a minimal promoter-mCherry cassette; synthesized 400-bp enhancers were cloned into the mCherry 3-prime UTR so enhancer activity was read by amplicon sequencing of ventricular RNA and AAV DNA. The source experiment used n=12 P0 biological replicates and n=28 P7/P28 biological replicates.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 38 definitions
- element_id
- GEO/source identifier for the tested enhancer element.
- mm10_coordinates
- 400-bp mouse genomic interval tested in the MPRA, on the mm10 assembly.
- group
- Study-defined broad class of tested element, such as Early P300, Late P300, Static P300, Positive Control, Negative Control, or Other.
- subgroup
- Study-defined finer annotation of the element class.
- p0_active
- Study binary activity call at P0; 1 indicates activity above the study negative-control threshold and 0 indicates inactive.
- p7_active
- Study binary activity call at P7; 1 indicates activity above the study negative-control threshold and 0 indicates inactive.
- p28_active
- Study binary activity call at P28; 1 indicates activity above the study negative-control threshold and 0 indicates inactive.
- p300_e12_5_signal
- P300 cardiomyocyte bioChIP-seq signal at E12.5.
- p300_e16_5_signal
- P300 cardiomyocyte bioChIP-seq signal at E16.5.
- p300_p0_signal
- P300 cardiomyocyte bioChIP-seq signal at P0.
- p300_p7_signal
- P300 cardiomyocyte bioChIP-seq signal at P7.
- p300_p14_signal
- P300 cardiomyocyte bioChIP-seq signal at P14.
- p300_p28_signal
- P300 cardiomyocyte bioChIP-seq signal at P28.
- p300_p42_signal
- P300 cardiomyocyte bioChIP-seq signal at P42.
- thra_p15_signal
- THRA ChIP-seq signal in P15 mouse heart from GSE125414.
- dna_rpm
- AAV-library DNA coverage for the element in reads per million, as reported by the study.
- p0_rna_rpm_median
- Median P0 ventricular reporter RNA coverage across 12 biological replicates, in RPM.
- p0_rna_rpm_sd
- Standard deviation of P0 reporter RNA coverage across 12 biological replicates, in RPM.
- p7_rna_rpm_median
- Median P7 ventricular reporter RNA coverage across 28 biological replicates, in RPM.
- p7_rna_rpm_sd
- Standard deviation of P7 reporter RNA coverage across 28 biological replicates, in RPM.
- p28_rna_rpm_median
- Median P28 ventricular reporter RNA coverage across 28 biological replicates, in RPM.
- p28_rna_rpm_sd
- Standard deviation of P28 reporter RNA coverage across 28 biological replicates, in RPM.
- p0_activity_rna_dna
- Median P0 enhancer activity, the reporter RNA/DNA ratio.
- p0_activity_sd
- Standard deviation of P0 RNA/DNA activity across biological replicates.
- p7_activity_rna_dna
- Median P7 enhancer activity, the reporter RNA/DNA ratio.
- p7_activity_sd
- Standard deviation of P7 RNA/DNA activity across biological replicates.
- p28_activity_rna_dna
- Median P28 enhancer activity, the reporter RNA/DNA ratio.
- p28_activity_sd
- Standard deviation of P28 RNA/DNA activity across biological replicates.
- p0_normalized_activity
- Median P0 activity normalized so the mean embryonic-stem-cell negative-control activity equals 1.
- p0_normalized_activity_sd
- Standard deviation of normalized P0 activity across biological replicates.
- p7_normalized_activity
- Median P7 activity normalized so the mean embryonic-stem-cell negative-control activity equals 1.
- p7_normalized_activity_sd
- Standard deviation of normalized P7 activity across biological replicates.
- p28_normalized_activity
- Median P28 activity normalized so the mean embryonic-stem-cell negative-control activity equals 1.
- p28_normalized_activity_sd
- Standard deviation of normalized P28 activity across biological replicates.
- dna_count_sum
- Sum of the three raw AAV-DNA replicate counts from the GEO processed count file; included for coverage traceability.
- p0_rna_count_median
- Median of the 12 raw P0 RNA replicate counts from the GEO processed count file.
- p7_rna_count_median
- Median of the 28 raw P7 RNA replicate counts from the GEO processed count file.
- p28_rna_count_median
- Median of the 28 raw P28 RNA replicate counts from the GEO processed count file.
Quality control
The study excluded elements with low AAV-DNA library coverage, normalized RNA/DNA activity to the mean embryonic-stem-cell negative-control activity at each time point, and used the negative-control 95th percentile/5% FDR activity calls. This package retained elements with DNA RPM >=5.0 and non-empty required fields; all 5,216 source elements passed this package filter. RNA/DNA activity values and study active flags are retained, including valid inactive measurements.
Curation notes
The supplemental Data S2 workbook and GEO GSE196346 P300 count table matched row-for-row. The processed table contains one row per assayed 400-bp element and preserves controls because they define the activity threshold. The article notes that MPRA measurements are episomal and that both mouse sexes were pooled; AAV9 transduction before E15.5 was inefficient, so earlier stages were not assayed.