Comprehensive native plant core-promoter STARR-seq in tobacco leaves
Synthetic promoter designs enabled by a comprehensive analysis of plant core promotersThe Arabidopsis, maize, and sorghum comprehensive native-promoter libraries were transiently delivered to Nicotiana benthamiana leaves. Promoter scores are summarized for no-enhancer and 35S-enhancer libraries in dark or 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 · 51 definitions
- promoter_id
- Gene or merged-gene identifier for the tested native 170-bp core promoter.
- source_species
- Plant species from which the promoter sequence was derived.
- gene_type
- Source annotation for the associated gene: protein_coding or miRNA.
- chromosome
- Source-annotation chromosome for the promoter interval.
- start
- Source-annotation start coordinate of the promoter interval.
- end
- Source-annotation end coordinate of the promoter interval.
- strand
- Orientation of the associated source gene/promoter in the source annotation.
- gc_content
- Fraction of G and C bases in the array-synthesized promoter sequence.
- has_annotated_5utr
- Whether the source gene has an annotated 5-prime UTR.
- library_barcode_count
- Number of barcodes linked to this promoter in Supplementary Table 1.
- library_mutations
- Sequence substitutions introduced during array synthesis to remove cloning restriction sites; blank when none were reported.
- sequence
- The 170-bp array-synthesized promoter sequence spanning -165 to +5 relative to the annotated TSS.
- 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 77,895 native promoter rows with a complete 170-bp sequence and at least one finite tobacco-leaf condition score after applying the WT/full-length construct filter; replicate-level scores are retained when available, and missing condition cells remain blank.
Curation notes
This table combines three source promoter species because the same tobacco-leaf assay system was used for each library. The assay organism is Nicotiana benthamiana; source promoter assemblies use Araport11, B73 RefGen v4, and NCBI_v3.43 annotations, so reference_genome is null at the combined-experiment level. Raw compact barcode counts and the authors' filtered subassemblies are retained under raw_data/source_counts and raw_data/filtered_subassembly_*.