A 461-element MPRAi library with 20 designed barcodes per element was delivered by systemic retro-orbital AAV-PHP.eB injection into adult C57BL/6J mice. DNA and RNA barcode counts from retained brain-region and peripheral-tissue samples quantify library representation and tissue-specific reporter activity.
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
UNMAPPED:multiple_mouse_tissues
Reference genome
Not reported / not applicable
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Non-integrating AAV-PHP.eB delivery of the pAAV-Hsp68-nls/mCherry-MPRAi reporter library; each 120-bp synthetic element has 20 designed 16-bp barcodes. DNA barcode recovery estimates construct representation and RNA/DNA barcode activity estimates reporter output. The processed log2_rna_dna_ratio is a derived library-size-normalized ratio with a +1 count pseudocount and is not the paper's MPRAnalyze/MAD score.
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 · 37 definitions
element_id
Unique enhancer, variant, or control construct identifier from Supplementary Table S2.
sequence
120-bp tested enhancer or control sequence.
sequence_length
Length of the tested sequence in nucleotides.
barcode_design_count
Number of designed barcodes for the element in the library; 20 for every element.
barcode_count_table_rows
Number of observed barcodes assigned to the element in the supplied DNA/RNA count matrices.
library_dna_detected_barcodes
Number of the element's designed barcodes marked dnaDetect=TRUE in Supplementary Table S2.
library_rna_detected_barcodes
Number of the element's designed barcodes marked rnaDetect=TRUE in Supplementary Table S2.
source
Top-level source label for the library construct.
sub_source
Detailed library design/control category from Supplementary Table S2.
design_group
Human-readable interpretation of the library design category.
control_status
Whether the construct is a positive control, negative control, candidate enhancer, or variant construct.
variant_family
Shared family identifier for linked allele or MEF2C constructs; blank for non-variant designs.
variant_state
State of a linked construct, such as reference, alternate, motif-disrupted, or shuffled.
paired_element_id
Element identifier(s) linked for direct allele or MEF2C construct comparison.
sample_id
Sample/run identifier from Supplementary Table S3.
tissue
Tissue or brain region reported for the sample.
replicate_or_animal
Animal number or replicate label reported for the sample.
nova_run
NovaSeq run number reported for the sample.
sample_rna_quality
Paper-reported RNA sample QC tier, blank when RNA was unavailable for the retained measurement.
sample_dna_quality
Paper-reported DNA sample QC tier, blank when DNA was unavailable for the retained measurement.
paper_qc_pass
TRUE for rows retained after the paper-reported sample/modality QC; failing entries are omitted.
measurement_type
Available retained modalities: paired_DNA_RNA, RNA_only, or DNA_only.
sample_total_dna_counts
Total DNA barcode counts across all observed barcode rows in the source matrix for this sample.
sample_total_rna_counts
Total RNA barcode counts across all observed barcode rows in the source matrix for this sample.
dna_count
Sum of raw DNA barcode counts for this element across its observed barcodes.
rna_count
Sum of raw RNA barcode counts for this element across its observed barcodes.
dna_cpm
Element DNA count per million total DNA barcode counts in the source sample.
rna_cpm
Element RNA count per million total RNA barcode counts in the source sample.
dna_barcodes_with_reads
Number of observed element barcodes with DNA count greater than zero.
rna_barcodes_with_reads
Number of observed element barcodes with RNA count greater than zero.
log2_rna_dna_ratio
Derived log2 of library-size-normalized RNA/DNA counts using a +1 count pseudocount; blank unless both retained modalities are available.
published_test_type
Published supplementary statistical test associated with the element or construct family, when available.
published_baseline_alpha
Baseline alpha value from the published MEF2C family-level test.
published_baseline_mad
Baseline median absolute deviation value from the published MEF2C family-level test.
published_test_statistic
Test statistic from Supplementary Table S7 or S8.
published_test_pvalue
P-value from Supplementary Table S7 or S8.
published_test_significant
TRUE/FALSE significance flag from S8 or derived as p<0.05 for S7.
Quality control
Applied the authors' arrayProc.2.1.1 restriction-site/barcode recognition and sample-level QC. The supplemental methods excluded low-RNA tissues (hypothalamus, muscle, kidney, lung, heart, ovaries, testes) and partial frontal cortex (PFC), and removed striatum animal 5, hippocampus animal 6, and striatum animal 2 DNA using the authors' dropout/outlier and read-depth criteria. The processed table retains only liver, M1, cortex, hippocampus, and striatum samples that remained after those exclusions, including the paper's medium-RNA-quality Liver_10_2, M1_5_1, and M1_6_1 rows because they were not listed as exclusions. All 461 elements had at least one mapped observed barcode; no element-level rows were removed.
Curation notes
Long-form table has 14,752 rows: 461 usable elements across 32 retained sample/library runs. The final library annotation contains 461 elements and 9,220 designed barcode records; the supplied Supplementary Tables S4/S5 used for aggregation contain 3,983 observed barcode rows, while the retained GEO mirrors contain all 9,220 designed barcode rows including zero/low-count rows. The GEO design text mentions an older 642-element count, but Supplementary Table S2 and the barcode matrices resolve to the final 461-element library. RNA-only second sequencing runs are retained as valid RNA measurements but have no derived RNA/DNA ratio because no matching DNA column exists. Published MEF2C paired-test values are carried across the three members of each MEF2C construct family; AD-associated S8 values are attached to the exact alternate/disrupt construct tested. The library includes mouse, human, macaque, zebra finch, bat, and synthetic controls, so no single reference assembly is assigned.