Core-promoter motif validation PROval STARR-seq in maize protoplasts
Synthetic promoter designs enabled by a comprehensive analysis of plant core promotersThe PROval library tested targeted TATA-box, no-TATA, and transcription-factor-binding-site promoter designs derived from Arabidopsis, maize, and sorghum. The library was 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.
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.
- 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.
- 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 633 PROval 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
Construct labels and sequences are taken from the authors' PROval validation annotation. The source_species field uses the authors' At/Zm/Sb codes, while target_organism identifies the maize-protoplast assay. 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.