Synthetic, motif-scan, and evolved promoter PROevo STARR-seq in tobacco leaves
Synthetic promoter designs enabled by a comprehensive analysis of plant core promotersThe PROevo library contains synthetic promoters, transcription-factor motif scans and combinations, targeted promoter-element controls, and native promoters evolved in silico for three or ten rounds. These designs from Arabidopsis, maize, and sorghum were transiently assayed in Nicotiana benthamiana leaves with or without the 35S enhancer under dark and light conditions across two biological replicates.
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
35S enhancer absent/present; dark or 16 h light/8 h dark after Agrobacterium infiltration
The assay used the episomal pPSup plant STARR-seq reporter: a 170-bp promoter sequence (-165 to +5 relative to the annotated TSS) was cloned upstream of a maize or sorghum histone 5-prime UTR, an ATG, GFP, and a 12-bp random barcode. Libraries with and without the upstream CaMV 35S enhancer were measured by sequencing barcode-containing input plasmid DNA and reporter mRNA; two independent biological replicates were performed for each library condition.
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 · 47 definitions
- construct_id
- Full validation-library construct label from the authors' barcode-to-sequence annotation.
- construct_gene
- Underlying source gene or synthetic promoter identifier, before the first period in construct_id.
- source_species
- Source species code for the validation construct: At, Zm, or Sb.
- design_category
- Motif, TF, synthetic, native-control, or evolution category encoded in the construct label.
- design_variant
- Specific mutation, motif combination, evolution model/round, or other design suffix encoded in the construct label.
- sequence
- The 170-bp array-synthesized validation, synthetic, or evolved promoter sequence.
- gc_content
- Fraction of G and C bases in the tested promoter sequence.
- library
- Validation library name used for the barcode counts: PROval or PROevo.
- no_enhancer_dark_rep1_log2
- Log2 frequency-normalized STARR-seq output/input barcode enrichment for biological replicate 1 (no 35S enhancer, dark).
- no_enhancer_dark_rep2_log2
- Log2 frequency-normalized STARR-seq output/input barcode enrichment for biological replicate 2 (no 35S enhancer, dark).
- no_enhancer_dark_mean_log2
- Mean of the available replicate-level promoter scores for no 35S enhancer, dark, normalized to the with-promoter/no-enhancer control.
- no_enhancer_dark_n_replicates
- Number of biological replicates with a valid promoter-level score for no 35S enhancer, dark.
- no_enhancer_dark_min_n_barcodes
- Minimum number of passing barcode assignments across the available replicates for no 35S enhancer, dark.
- no_enhancer_dark_rep1_n_barcodes
- Number of promoter barcodes passing the input/output count cutoff in replicate 1 (no 35S enhancer, dark).
- no_enhancer_dark_rep2_n_barcodes
- Number of promoter barcodes passing the input/output count cutoff in replicate 2 (no 35S enhancer, dark).
- no_enhancer_dark_rep1_sd
- Sample standard deviation of barcode-level normalized enrichment in replicate 1 (no 35S enhancer, dark); blank when fewer than two barcodes pass QC.
- no_enhancer_dark_rep2_sd
- Sample standard deviation of barcode-level normalized enrichment in replicate 2 (no 35S enhancer, dark); blank when fewer than two barcodes pass QC.
- with_enhancer_dark_rep1_log2
- Log2 frequency-normalized STARR-seq output/input barcode enrichment for biological replicate 1 (35S enhancer, dark).
- with_enhancer_dark_rep2_log2
- Log2 frequency-normalized STARR-seq output/input barcode enrichment for biological replicate 2 (35S enhancer, dark).
- with_enhancer_dark_mean_log2
- Mean of the available replicate-level promoter scores for 35S enhancer, dark, normalized to the with-promoter/no-enhancer control.
- with_enhancer_dark_n_replicates
- Number of biological replicates with a valid promoter-level score for 35S enhancer, dark.
- with_enhancer_dark_min_n_barcodes
- Minimum number of passing barcode assignments across the available replicates for 35S enhancer, dark.
- with_enhancer_dark_rep1_n_barcodes
- Number of promoter barcodes passing the input/output count cutoff in replicate 1 (35S enhancer, dark).
- with_enhancer_dark_rep2_n_barcodes
- Number of promoter barcodes passing the input/output count cutoff in replicate 2 (35S enhancer, dark).
- with_enhancer_dark_rep1_sd
- Sample standard deviation of barcode-level normalized enrichment in replicate 1 (35S enhancer, dark); blank when fewer than two barcodes pass QC.
- with_enhancer_dark_rep2_sd
- Sample standard deviation of barcode-level normalized enrichment in replicate 2 (35S enhancer, dark); blank when fewer than two barcodes pass QC.
- no_enhancer_light_rep1_log2
- Log2 frequency-normalized STARR-seq output/input barcode enrichment for biological replicate 1 (no 35S enhancer, 16 h light/8 h dark).
- no_enhancer_light_rep2_log2
- Log2 frequency-normalized STARR-seq output/input barcode enrichment for biological replicate 2 (no 35S enhancer, 16 h light/8 h dark).
- no_enhancer_light_mean_log2
- Mean of the available replicate-level promoter scores for no 35S enhancer, 16 h light/8 h dark, normalized to the with-promoter/no-enhancer control.
- no_enhancer_light_n_replicates
- Number of biological replicates with a valid promoter-level score for no 35S enhancer, 16 h light/8 h dark.
- no_enhancer_light_min_n_barcodes
- Minimum number of passing barcode assignments across the available replicates for no 35S enhancer, 16 h light/8 h dark.
- no_enhancer_light_rep1_n_barcodes
- Number of promoter barcodes passing the input/output count cutoff in replicate 1 (no 35S enhancer, 16 h light/8 h dark).
- no_enhancer_light_rep2_n_barcodes
- Number of promoter barcodes passing the input/output count cutoff in replicate 2 (no 35S enhancer, 16 h light/8 h dark).
- no_enhancer_light_rep1_sd
- Sample standard deviation of barcode-level normalized enrichment in replicate 1 (no 35S enhancer, 16 h light/8 h dark); blank when fewer than two barcodes pass QC.
- no_enhancer_light_rep2_sd
- Sample standard deviation of barcode-level normalized enrichment in replicate 2 (no 35S enhancer, 16 h light/8 h dark); blank when fewer than two barcodes pass QC.
- with_enhancer_light_rep1_log2
- Log2 frequency-normalized STARR-seq output/input barcode enrichment for biological replicate 1 (35S enhancer, 16 h light/8 h dark).
- with_enhancer_light_rep2_log2
- Log2 frequency-normalized STARR-seq output/input barcode enrichment for biological replicate 2 (35S enhancer, 16 h light/8 h dark).
- with_enhancer_light_mean_log2
- Mean of the available replicate-level promoter scores for 35S enhancer, 16 h light/8 h dark, normalized to the with-promoter/no-enhancer control.
- with_enhancer_light_n_replicates
- Number of biological replicates with a valid promoter-level score for 35S enhancer, 16 h light/8 h dark.
- with_enhancer_light_min_n_barcodes
- Minimum number of passing barcode assignments across the available replicates for 35S enhancer, 16 h light/8 h dark.
- with_enhancer_light_rep1_n_barcodes
- Number of promoter barcodes passing the input/output count cutoff in replicate 1 (35S enhancer, 16 h light/8 h dark).
- with_enhancer_light_rep2_n_barcodes
- Number of promoter barcodes passing the input/output count cutoff in replicate 2 (35S enhancer, 16 h light/8 h dark).
- with_enhancer_light_rep1_sd
- Sample standard deviation of barcode-level normalized enrichment in replicate 1 (35S enhancer, 16 h light/8 h dark); blank when fewer than two barcodes pass QC.
- with_enhancer_light_rep2_sd
- Sample standard deviation of barcode-level normalized enrichment in replicate 2 (35S enhancer, 16 h light/8 h dark); blank when fewer than two barcodes pass QC.
- enhancer_effect_dark_log2
- Difference between the with-35S-enhancer and no-enhancer dark mean promoter scores (with enhancer minus no enhancer).
- light_dependency_no_enhancer_log2
- Difference between light and dark mean promoter scores in the no-enhancer library (light minus dark).
- light_dependency_with_enhancer_log2
- Difference between light and dark mean promoter scores in the 35S-enhancer library (light minus dark).
Quality control
The authors discarded promoter-barcode subassemblies with fewer than 5 assembly reads and barcode observations with fewer than 5 input or output reads. The package retained 4,513 PROevo constructs with a complete 170-bp sequence and at least one finite tobacco-leaf condition score after applying the WT/full-length construct filter; construct-level scores are summarized from the available barcode medians across two biological replicates.
Curation notes
PROevo is a heterogeneous design library, so design_category and design_variant are parsed from the authors' full construct labels. It includes the synthetic-promoter and evolved-promoter designs reported in Supplementary Tables 6 and 7 as well as additional motif-scan/combination and promoter-element validation constructs. The assay organism is tobacco; source promoter species are retained separately.