Improved STARR-seq (iSTARR-seq) in Arabidopsis thaliana leaf protoplasts
Resolving a Systematic Error in STARR-seq for Quantitative Enhancer Activity MappingThe same genome-wide 500–800-bp Arabidopsis genomic-fragment library was assayed in leaf protoplasts with the improved iSTARR-seq reverse-transcription design. Merged reporter cDNA and plasmid DNA signal from two biological replicates quantify activity while recovering transcripts terminated at internal alternative polyadenylation sites.
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
Improved episomal STARR-seq (iSTARR-seq) using the same pPBI221-based CMV 35S mini-promoter/intron/GFP reporter, but an N6T18RV reverse-transcription primer containing eighteen deoxythymidines and six random nucleotides. This design captures self-transcripts independent of whether polyadenylation occurs at the designated PAS or an internal alternative PAS. Two biological replicates each were generated for plasmid and cDNA libraries; iSTARR cDNA includes aST and dST transcript classes.
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 trimmed the 20-bp 5-prime oligo-dT sequence and 30-bp low-quality 3-prime bases from both paired-end reads, aligned to TAIR10 with the same Bowtie2 settings, removed duplicates with Picard MarkDuplicates, and retained paired high-quality alignments with samtools view -f 2 -q 5. Six indexed iSTARR plasmid sub-libraries per replicate were merged after library 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 (2.97544674), 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 4,956 iSTARR-seq enhancers and 8,499,975 filtered aST reads after its own analysis. 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.