AAV-MPRA screen of chamber-selective enhancer candidates
In Vivo Dissection of Chamber-Selective Enhancers Reveals Estrogen-Related Receptor as a Regulator of Ventricular Cardiomyocyte IdentityA pooled AAV9 MPRA library of 400-bp mouse candidate regulatory regions was delivered to P0 pups and assayed in purified neonatal atrial and ventricular cardiomyocytes at P7. Five DNA, five atrial RNA, and five ventricular RNA replicates quantify enhancer activity and chamber 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 library delivered at P0 and heart chambers collected at P7
The AAV-MPRA uses a STARR-seq-style reporter with each candidate enhancer in the 3′ UTR downstream of an hsp68 minimal promoter and mCherry. Each 400-bp region was synthesized as a 230-nt self-priming oligonucleotide pair. Atria and ventricles were analyzed separately from the same library; GEO supplies deduplicated read counts for each region and sample.
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 · 56 definitions
- region_id
- Exact GEO region identifier containing the occupancy design token and mm10 coordinate.
- chromosome
- Chromosome parsed from the reported mm10 coordinate.
- start
- Reported region start coordinate; the source uses a 400-bp span where end minus start equals 400.
- end
- Reported region end coordinate; the source uses a 400-bp span where end minus start equals 400.
- element_length_bp
- Coordinate span calculated as end minus start.
- occupancy_design
- Source design/occupancy token before the coordinate, encoding chamber-specific or shared TF/P300 features.
- library_group
- GEO library category: TF1-2, TF3-4, MTF or P300, spMTF or spP300, or Neg.
- dna_count_rep1
- Deposited AAV-genome DNA read count for DNA replicate 1.
- dna_count_rep2
- Deposited AAV-genome DNA read count for DNA replicate 2.
- dna_count_rep3
- Deposited AAV-genome DNA read count for DNA replicate 3.
- dna_count_rep4
- Deposited AAV-genome DNA read count for DNA replicate 4.
- dna_count_rep5
- Deposited AAV-genome DNA read count for DNA replicate 5.
- atrium_rna_count_rep1
- Deposited atrial RNA read count for biological replicate 1.
- atrium_rna_count_rep2
- Deposited atrial RNA read count for biological replicate 2.
- atrium_rna_count_rep3
- Deposited atrial RNA read count for biological replicate 3.
- atrium_rna_count_rep4
- Deposited atrial RNA read count for biological replicate 4.
- atrium_rna_count_rep5
- Deposited atrial RNA read count for biological replicate 5.
- ventricle_rna_count_rep1
- Deposited ventricular RNA read count for biological replicate 1.
- ventricle_rna_count_rep2
- Deposited ventricular RNA read count for biological replicate 2.
- ventricle_rna_count_rep3
- Deposited ventricular RNA read count for biological replicate 3.
- ventricle_rna_count_rep4
- Deposited ventricular RNA read count for biological replicate 4.
- ventricle_rna_count_rep5
- Deposited ventricular RNA read count for biological replicate 5.
- 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.
- ventricle_rna_fpm_rep5
- ventricular RNA replicate 5 read count normalized to fragments per million within that sample.
- dna_fpm_mean
- Mean DNA fragments per million across the five DNA replicates.
- dna_fpm_max
- Maximum DNA fragments per million across the five DNA replicates; the package QC gate is ≥5.
- atrium_rna_fpm_mean
- Mean atrial RNA fragments per million across five RNA replicates.
- ventricle_rna_fpm_mean
- Mean ventricular RNA fragments per million across five RNA 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 per-replicate log2 RNA/DNA scores versus zero.
- atrium_activity_fdr
- Benjamini-Hochberg FDR for the atrial activity p-values among QC-passed regions.
- ventricle_activity_p_value
- Two-sided one-sample t-test p-value for ventricular per-replicate log2 RNA/DNA scores versus zero.
- ventricle_activity_fdr
- Benjamini-Hochberg FDR for the ventricular activity p-values among QC-passed regions.
- chamber_selectivity_p_value
- Welch two-sample p-value comparing atrial and ventricular per-replicate log2 RNA/DNA scores.
- chamber_selectivity_fdr
- Benjamini-Hochberg FDR for the chamber-selectivity p-values among QC-passed regions.
- active_atrium
- Derived atrial activity call: positive activity score and FDR <0.05.
- active_ventricle
- Derived ventricular activity call: positive activity score and FDR <0.05.
- active_any
- TRUE when either chamber has a derived active call.
- chamber_selective_class
- Derived activity class using active calls, |atrial minus ventricular activity| >0.58, and selectivity FDR <0.05.
- qc_pass
- TRUE for every row retained after the source DNA-coverage filter.
Quality control
The article states that candidate regions with low AAV-genome DNA coverage were removed. Normalizing each of the five DNA libraries to FPM and retaining a region when at least one DNA replicate was ≥5 FPM reproduces the paper’s reported surviving set exactly: 2,160 candidate regions plus 479 negative-control regions (2,639 total from 3,820 deposited rows). Activity scores are mean per-replicate log2((RNA FPM + 0.5)/(DNA FPM + 0.5)); derived activity and chamber-selectivity p-values use two-sided t-tests and are BH-adjusted. Rows failing the DNA gate are absent from table.csv.
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 GEO aggregate has 3,820 rows and five library groups; this differs from the broader design totals described in the article, but the reported post-coverage counts are recovered exactly. GEO count tables do not include the full 400-bp sequences, so region coordinates and source occupancy tokens are retained while sequence strings are not fabricated. The article’s own active/CSE calls use its custom MPRA analysis; the p-values/FDR and classes in this package are transparent replicate-level summaries of the deposited counts.