Synthetic STARR-seq of single-nucleotide ABRE variants in ABA-treated Nicotiana benthamiana leaves
High-throughput quantitative assessment of ABA-responsive elements at single-nucleotide resolutionA synthetic STARR-seq library tested randomized 10-bp ABRE sequences covering the ACGT core and the flanking positions in transiently infiltrated Nicotiana benthamiana leaves. Three biological replicates were measured under matched untreated-control and 25 μM ABA-treated conditions, and the processed table contains the 2,554 variants with complete source activity values.
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
25 μM abscisic acid (ABA) for 4 h after 48 h darkness; matched untreated controls
The episomal pGreenII 0800-LUC construct placed the synthetic ABRE-containing sequence upstream of the 35S minimal promoter; a 12-bp random barcode was placed before the second codon of the firefly luciferase reporter. A 50-bp regulatory fragment derived from the Arabidopsis ABI1 promoter was randomized either across the four core positions or across the six flanking positions, producing one ACGT-core library and four ACGT-flank sublibraries; a separate 35S enhancer library served as an assay control. Pooled plasmids were introduced into Agrobacterium tumefaciens GV3101 carrying pSoup and transiently delivered to tobacco leaves by vacuum agroinfiltration. Reporter RNA barcode abundance was normalized to input plasmid DNA; the source supplement reports three control and three ABA-treated biological replicates.
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 · 21 definitions
- element_id
- Unique package identifier formed as library:ABRE sequence.
- library
- Source Table S3 library label: ACGT-core or the pooled ACGT-flank libraries.
- abre_sequence
- The 10-bp synthetic ABRE sequence tested in the reporter library.
- variable_region
- Randomized sequence positions (1-based): 4-7 for core variants or 1-3 and 8-10 for flank variants.
- control_1_rna_dna
- Source Table S3 RNA/DNA transcriptional-strength value for control biological replicate 1.
- control_2_rna_dna
- Source Table S3 RNA/DNA transcriptional-strength value for control biological replicate 2.
- control_3_rna_dna
- Source Table S3 RNA/DNA transcriptional-strength value for control biological replicate 3.
- aba_1_rna_dna
- Source Table S3 RNA/DNA transcriptional-strength value for ABA biological replicate 1.
- aba_2_rna_dna
- Source Table S3 RNA/DNA transcriptional-strength value for ABA biological replicate 2.
- aba_3_rna_dna
- Source Table S3 RNA/DNA transcriptional-strength value for ABA biological replicate 3.
- control_mean_rna_dna
- Arithmetic mean of the three control RNA/DNA activity values.
- aba_mean_rna_dna
- Arithmetic mean of the three ABA RNA/DNA activity values.
- aba_minus_control_mean
- ABA mean activity minus control mean activity.
- aba_over_control_fold_change
- ABA mean activity divided by control mean activity.
- log2_aba_over_control_mean
- Base-2 logarithm of the derived ABA-over-control mean fold change.
- aba_log2_fold_change_author
- Author-reported log2(FoldChange) from Table S4, blank for variants not listed there.
- aba_p_value_author
- Author-reported DESeq2 p-value from Table S4, blank for variants not listed there.
- aba_response_class_author
- Author-reported Table S4 response class, Enhancing or Blunting.
- aba_responsive_in_table_s4
- Boolean indicating whether the variant is present in the author-reported responsive-variant Table S4.
- qc_pass
- Boolean indicating that the row passed source/package extraction QC and was retained.
- source_table
- Supplementary table(s) contributing values to the row.
Quality control
The authors removed ABRE-barcode associations with DNA read counts below 10 and retained only ABRE variants linked to at least 5 unique barcodes. RNA barcodes with read counts below 5 were discarded, and the paper reports three biological replicates with Pearson correlation coefficients of 0.945 for control and 0.975 for ABA treatment. The paper used DESeq2 with p < 0.05 and fold change > 1.2 to call ABA-responsive variants. Package QC retained 2,554 of the 2,554 rows in Table S3: each retained row had a valid 10-bp uppercase sequence and finite, nonnegative values in all six replicate RNA/DNA activity columns; incomplete or nonnumeric rows were excluded during extraction. Table S4 p-values and calls are preserved as supplied and were not recomputed or used to remove nonsignificant variants.
Curation notes
The paper describes one STARR-seq assay containing one ACGT-core library, four ACGT-flank sublibraries, and a separate 35S enhancer control library; the 35S library is an assay control and is not represented as a separate experiment. Table S3 collapses the four flank sublibraries into the single ACGT-flank label and provides variant-level activity values for 220 core and 2,334 flank variants, matching the RNA-seq recovery counts in the main text. Table S4 contains 116 variants (22 core and 94 flank) that match Table S3 by library and sequence and adds the author-reported ABA response statistics. The package preserves the source p-values without claiming they are FDR-adjusted. The synthetic ABI1-derived fragment has no stated genomic assembly or coordinate, so reference_genome and region_of_interest are null. The tobacco leaf biosample could not be resolved to the requested Cell Ontology/UBERON vocabulary and is explicitly marked UNMAPPED. Raw sequencing reads were not packaged; SRA run metadata and the open supporting-information PDF are included instead.