An in vivo AAV9 MPRA tested 190-bp wild-type and motif-shuffled mutant pairs centered on candidate nuclear-receptor motifs in Early and Late P300 regions, along with positive and negative controls. The library was delivered subcutaneously to P0 pups and ventricular reporter RNA was measured at P7 across 14 biological replicates.
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.
Organism
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
CL:0000746
Reference genome
mm10
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Nuclear-receptor motif ablation by sequence shuffling; P0 AAV9 delivery with P7 ventricular collection
Self-complementary AAV9 episomal minimal-promoter-mCherry reporter; 190-bp wild-type regions and motif-shuffled mutants were synthesized as paired oligos and assayed by ventricular reporter RNA/AAV-DNA amplicon sequencing. The source experiment used n=14 biological replicates; the study reported paired t-test FDR and absolute fold-change criteria for motif effects.
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 · 27 definitions
element_id
Unique enhancer sequence identifier from the study/GEO count table, such as LP-WT_294 or LP-Mut_294.
pair_id
Study-provided WT-mutant pair identifier; blank when the source workbook used '-'.
mm10_coordinates
190-bp mouse genomic interval centered on the candidate nuclear-receptor motif, on mm10.
sequence
Tested oligonucleotide sequence, including the shuffled motif sequence for mutant elements.
group
Study-defined broad class of the sequence, such as Early P300, Late P300, Pos. Ctrl, Neg. Ctrl, or Other.
subgroup
Study-defined finer annotation of the sequence class.
type
Allelic/design state of the sequence: Wildtype or Mutant.
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, where supplied by the study.
dna_rpm
AAV-library DNA coverage for the sequence in reads per million, as reported by the study.
rna_rpm_median
Median P7 ventricular reporter RNA coverage across 14 biological replicates, in RPM.
rna_rpm_sd
Standard deviation of P7 reporter RNA coverage across 14 biological replicates, in RPM.
activity_rna_dna
Median P7 enhancer activity, the reporter RNA/DNA ratio.
activity_sd
Standard deviation of P7 RNA/DNA activity across biological replicates.
normalized_activity
Median P7 activity normalized so the mean negative-control activity equals 1.
normalized_activity_sd
Standard deviation of normalized P7 activity across biological replicates.
p7_activity_active
Package-derived activity call: 1 when normalized activity is above the retained negative-control 95th percentile (2.15611004375), otherwise 0.
paired_mutant_activity_fold_change
Study-reported activity fold change for the paired mutant relative to the active wild-type enhancer; populated on source rows where reported, and values below 1 indicate reduced mutant activity.
paired_bh_fdr
Study-reported Benjamini-Hochberg adjusted P value for the WT-mutant activity comparison, populated where reported.
dna_count_sum
Sum of the three raw AAV-DNA replicate counts from the GEO processed count file; included for coverage traceability.
rna_count_median
Median of the 14 raw P7 RNA replicate counts from the GEO processed count file.
Quality control
The study excluded regions with low AAV-DNA library coverage and used the negative-control 95th percentile as the activity threshold. This package applies a transparent DNA RPM >=5.0 coverage floor to the 7,284 source rows, removes 124 low-coverage rows, and retains 7,160 rows. The normalized P7 negative-control 95th percentile in the retained source rows is 2.15611004375; p7_activity_active is derived by comparing normalized activity to this threshold. Inactive elements are retained, while source '-' values are blanked and unprovided pair IDs are not inferred.
Curation notes
The supplemental Data S3 workbook and GEO GSE196346 NR count table matched row-for-row. The table is sequence-level so WT and mutant constructs remain separate rows, joined by the source pair_id where available. The source contains 11 retained dynamic rows with no explicit pair ID; those rows are preserved without inventing a pair mapping. The article notes that MPRA measurements are episomal and that both mouse sexes were pooled.