In vivo AAV MPRA of murine cardiac enhancer candidates
A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancersA pooled library of 400 bp genomic regions and negative controls was cloned into a self-complementary AAV reporter carrying a minimal MLC2v promoter and mCherry with the enhancer in the 3' UTR. The library was injected into wild-type CFW pups at P0, and P7 ventricular RNA activity was quantified relative to untransduced library DNA abundance.
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
AAV MPRA library delivery (2e11 viral genomes per pup, subcutaneous at P0); no additional biological treatment
Agilent oligonucleotide pool; each element was assembled from two 230 bp single-stranded oligos with a 20 bp overlap into approximately 400 bp enhancers. The pooled self-complementary AAV library used an MLC2v minimal promoter-mCherry reporter with the enhancer in the 3' UTR; 28 wild-type CFW pups were injected, ventricular apexes were harvested at P7, and RNA and triplicate untransduced library DNA were sequenced as paired-end 2x150 bp NextSeq500 libraries.
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 · 17 definitions
- element_id
- Unique row-level identifier assigned during packaging
- source_row
- Original worksheet row number in SourceData_Main.xlsx, Fig.4g
- source_id
- Original ID field from the source workbook; not globally unique
- chromosome
- mm9 chromosome for the tested genomic interval
- start
- Reported interval start coordinate
- end
- Reported interval end coordinate
- interval_length_bp
- end minus start from the reported coordinates
- group
- Original Fig.4g library group label
- group_label
- Readable interpretation of the original group label
- element_class
- Candidate enhancer or negative control
- p7_cm_p300_binding
- Source P7 CM P300 binding value; units were not specified
- dna_average
- Mean untransduced AAV DNA abundance reported for the element; used for the published low-frequency filter
- dna_rank
- Rank of the element by DNA abundance in the source table
- rna_average
- Mean P7 ventricular RNA read abundance reported for the element
- rna_dna_ratio
- Published RNA:DNA enhancer activity ratio
- log2_rna_dna
- log2 transformation of the published RNA:DNA ratio
- above_es_95pct_activity
- TRUE when RNA:DNA ratio exceeds the derived 95th percentile of ES-control ratios (0.8714258675)
Quality control
The authors removed adapters, retained concordantly aligned paired reads with insert lengths of 395-405 bp, counted elements with BedTools, averaged untransduced AAV DNA abundance across three DNA preparations, and excluded elements below 5 RPM. The source Fig.4g table contains 1,982 finite rows, all with DNA average >=5.114788487; all 1,982 rows were retained. The 5% activity flag in the table is a derived comparison to the ES-control 95th percentile, not a per-element p-value.
Curation notes
The packaged experiment is the pooled MPRA described in Fig.4g-h; the 12 individually tested AAV9 enhancers are not a separate MPRA experiment. The source sheet contains 1,982 reported rows from a 2,700-region synthesized library. Its source_id field has 1,522 unique values with 426 duplicated ID groups, and seven coordinates repeat; row-level element_id and source_row preserve every reported record without collapsing or silently deduplicating it. Intervals have reported end-start values of either 399 or 400 bp, which are preserved. The mappings of negative to VISTA forebrain H3K27ac controls and ES to embryonic-stem-cell P300 controls are based on the paper's Methods and Supplementary Fig. 12. The activity flag uses the linearly interpolated ES-control 95th percentile of the source RNA:DNA ratios and is provided for researcher convenience.