AAV-STARR-seq enhancer screen in mouse neocortex
An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivoAn unbiased library of approximately 700-bp mouse genomic fragments from nine BAC-covered loci spanning about 3 Mb was cloned downstream of a 4.26 minimal promoter in a self-transcribing STARR-seq reporter and packaged in AAV8. The library was injected into the dorsal neocortex of adult male C57BL/6JRj mice; poly(A) RNA from five analyzed animals was compared with three AAV-packaged viral-DNA input replicates to identify reproducible enhancer peaks.
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
This is an AAV-delivered STARR-seq implementation: genomic fragments are inserted downstream of the 4.26 minimal promoter and active fragments transcribe their own sequence, so the screen does not use synthetic DNA barcodes. A self-complementing AAV library was packaged in AAV8 capsids, delivered stereotactically, and measured from poly(A) RNA in homogenized neocortex relative to AAV-packaged viral-DNA input; five mice were used for final peak calling and mouse 6 was excluded for low sequencing depth.
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 · 26 definitions
- peak_id
- Peak identifier from the official GEO final common-peak BED file.
- chromosome
- mm10 chromosome for the peak.
- start_0based
- 0-based inclusive BED start coordinate.
- end_0based_exclusive
- 0-based exclusive BED end coordinate.
- width_bp
- Peak interval width in base pairs.
- starrpeaker_bed_score
- BED score field from the GEO final peak file, retained as supplied; not recalculated or interpreted as a p-value.
- screened_gene
- Target gene associated with the BAC-covered locus; this is not a claim that every peak regulates that gene.
- screened_bac_region
- Broad BAC interval containing the peak, from Supplementary Table 1.
- rna_mouse_1_mean_signal
- Mean normalized RNA BigWig signal over the peak for mouse 1 (GSM5906706).
- rna_mouse_2_mean_signal
- Mean normalized RNA BigWig signal over the peak for mouse 2 (GSM5906707).
- rna_mouse_3_mean_signal
- Mean normalized RNA BigWig signal over the peak for mouse 3 (GSM5906708).
- rna_mouse_4_mean_signal
- Mean normalized RNA BigWig signal over the peak for mouse 4 (GSM5906709).
- rna_mouse_5_mean_signal
- Mean normalized RNA BigWig signal over the peak for mouse 5 (GSM5906710).
- mean_rna_signal
- Arithmetic mean of the five analyzed mouse RNA peak signals.
- input_dna_1_mean_signal
- Mean normalized AAV-packaged viral-DNA input BigWig signal for input replicate 1 (GSM5906712).
- input_dna_2_mean_signal
- Mean normalized AAV-packaged viral-DNA input BigWig signal for input replicate 2 (GSM5906713).
- input_dna_3_mean_signal
- Mean normalized AAV-packaged viral-DNA input BigWig signal for input replicate 3 (GSM5906714).
- mean_input_dna_signal
- Arithmetic mean of the three input-DNA technical-replicate peak signals.
- rna_over_input_ratio
- Mean RNA signal divided by mean input-DNA signal; calculated without a pseudocount because all retained intervals had positive signal.
- log2_rna_over_input
- Base-2 logarithm of rna_over_input_ratio; a derived enhancer-activity score analogous to the paper's RNA/input log2 fold-change signal.
- min_rna_coverage_fraction
- Minimum fraction of peak bases covered by the five RNA BigWig tracks.
- min_input_coverage_fraction
- Minimum fraction of peak bases covered by the three input-DNA BigWig tracks.
- analyzed_rna_mouse_count
- Number of RNA biological replicates used for the final peak set and mean signal (5).
- input_dna_replicate_count
- Number of AAV-packaged viral-DNA technical input replicates used for quantification (3).
- final_peak_set
- TRUE for rows retained from the common peak set after BAC-boundary filtering.
- qc_pass
- TRUE for rows passing the documented source and processing filters.
Quality control
The authors ran FastQC, mapped paired-end reads to mm10 with bowtie2 (--very-sensitive, end-to-end, --maxins 1000), retained proper pairs with MAPQ >=3 using samtools, and removed duplicate reads with Picard MarkDuplicates. BigWig tracks were scaled to 1,000,000 divided by total mapped reads. Mouse 6 was excluded because its sequencing and mapped-read depth was less than 10% of the other RNA samples. STARRPeaker used 500-bp windows stepped by 100 bp with GC content and RNA secondary-structure covariates; per-RNA calls were compared with each of three input-DNA technical replicates, retained when detected in more than one input replicate, and the final set was restricted to peaks common to all five analyzed mice. For the processed table, the official final peak BED was additionally restricted to intervals fully contained within the nine BAC ranges from Supplementary Table 1; peak_077 and peak_485 crossed outer BAC boundaries and were omitted, leaving 483 rows matching the reported candidate-enhancer count. No additional signal-coverage cutoff was imposed because the supplied BigWig tracks are normalized coverage tracks and the official common-peak calls are the study's element-level QC; coverage fractions are retained as audit columns, and mean0 signal includes uncovered bases as zero.
Curation notes
The study is AAV-STARR-seq rather than a barcode-based MPRA: active fragments are self-transcribing and therefore have no synthetic barcode or variant-allele contrast. The untouched GEO final peak file is preserved in raw_data and contains 485 rows; two intervals (peak_077 and peak_485) extend beyond the outer BAC coordinates, so table.csv retains the 483 fully contained rows that agree with the paper's reported result. Mouse 6 and its RNA BigWig are retained for provenance but were not used in table.csv. Signal summaries were derived with UCSC bigWigAverageOverBed from the authors' per-million-normalized BigWig tracks; mean0 was used so uncovered bases contribute zero. The table contains peak-level signal summaries, not original read counts or caller p-values; coverage fractions are provided to make the source-track coverage visible.