Conventional STARR-seq in Arabidopsis thaliana leaf protoplasts
Resolving a Systematic Error in STARR-seq for Quantitative Enhancer Activity MappingA genome-wide library of 500–800-bp sonicated A. thaliana genomic fragments was cloned into a pPBI221-based self-transcribing reporter and transfected into leaf protoplasts. The experiment compares merged reporter cDNA and plasmid DNA signal from two biological replicates to quantify enhancer 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.
Perturbation & assay details
Basal / Untreated
Original/conventional episomal self-transcribing assay with a CMV 35S mini-promoter, intron, and GFP reporter; test fragments were 500–800 bp. Poly(A)+ reporter RNA was reverse-transcribed with the conventional reverse primer, so transcripts terminated at internal alternative polyadenylation sites can be missed. Two biological replicates each were generated for plasmid and cDNA libraries.
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 · 17 definitions
- element_id
- Stable identifier assigned to a QC-passing reconstructed activity window.
- chromosome
- TAIR10 chromosome name.
- start
- 0-based inclusive start of the 500-bp window.
- end
- 0-based exclusive end of the 500-bp window (BED convention).
- width
- Window width in base pairs (500 for every row).
- summit_start
- 0-based inclusive start of the strongest 100-bp subwindow within the element.
- summit_end
- 0-based exclusive end of the strongest 100-bp subwindow.
- cdna_mean_signal
- Mean normalized merged reporter-cDNA BigWig signal over the 500-bp element.
- plasmid_mean_signal
- Mean normalized merged plasmid-input BigWig signal over the 500-bp element.
- activity_ratio
- cDNA mean signal divided by plasmid mean signal.
- log2_activity
- Log2-transformed activity_ratio.
- summit_cdna_mean_signal
- Mean cDNA signal over the strongest 100-bp subwindow.
- summit_plasmid_mean_signal
- Mean plasmid signal over that same 100-bp subwindow.
- summit_enrichment
- Summit cDNA/plasmid signal ratio.
- qc_input_floor
- Minimum required 500-bp plasmid mean signal.
- qc_activity_threshold
- Empirical 99.5th-percentile 500-bp activity-ratio threshold among windows meeting the input floor.
- qc_pass
- Boolean marker; every emitted row passed the stated filters.
Quality control
Authors aligned paired-end reads to TAIR10 with Bowtie2 (--no-discordant -X 2000), removed duplicates with Picard MarkDuplicates, and retained paired high-quality alignments with samtools view -f 2 -q 5. Replicate cDNA and plasmid libraries were merged after high correlation/coverage QC. Original enhancer calling used BasicSTARRseq (minQuantile=0.9, peakWidth=500, maxPval=0.001) and retained full-region activity >1, summit activity >=1.3, p<0.001, and FDR<0.001. For this package, the deposited merged BigWig tracks were scanned in 500-bp windows every 50 bp on chr1–chr5; rows required finite values, plasmid mean signal >=0.5, activity ratio >= the empirical 99.5th percentile (1.93836031), summit enrichment >=1.3, and greedy non-maximum suppression leaving >=500 bp between starts. chrC and chrM were excluded from the nuclear enhancer table. Only rows passing all filters are included.
Curation notes
The GEO series supplies merged normalized BigWig tracks rather than the authors’ machine-readable BasicSTARRseq peak table. This table is therefore a reproducible high-confidence reconstruction from the deposited merged tracks, not a re-publication of author p-values/FDR. The original study reported 15,862 conventional STARR-seq enhancers after its own peak calling. Signal units are the source BigWig units; the source combines two biological replicates. The whole-genome designation reflects the library, while the processed table intentionally excludes organellar chromosomes.