The 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 electroporated into Zea mays B73 leaf protoplasts and assayed in the dark with or without the 35S enhancer 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.
Organism
NCBITaxon:4577
Taxonomy ID
NCBITaxon:4577
Biosample
UNMAPPED:Zea_mays_leaf_protoplast
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
35S enhancer absent/present; 16 h dark after electroporation
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 · 27 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.
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.
enhancer_effect_dark_log2
Difference between the with-35S-enhancer and no-enhancer dark mean promoter scores (with enhancer minus no enhancer).
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 4,405 PROevo constructs with a complete 170-bp sequence and at least one finite maize-protoplast 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 maize; source promoter species are retained separately. For the protoplast replicate-2 libraries, the authors' workflow reuses the replicate-1 input plasmid count file; this convention is preserved by the processing script.