An episomal, barcoded luciferase MPRA screened 11,180 synthetic 160-bp promoter fragments derived from 1,118 fruit-specific tomato genes, with transient Agrobacterium delivery to Micro-Tom fruit at mature-green, breaker, and red-ripe stages and to leaves. The packaged table is the study's 2,436-row active-enhancer model dataset, with deposited mean leaf and fruit activity targets rather than stage-specific count matrices.
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:4081
Taxonomy ID
NCBITaxon:4081
Biosample
UNMAPPED:tomato_fruit_and_leaf_tissue
Reference genome
SL4.0
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The pGreenII 0800-LUC construct placed each candidate fragment upstream of a 51-bp CaMV 35S minimal promoter, a short synthetic synJ 5' UTR, and firefly luciferase, with a 15-bp random barcode. The library was delivered using Agrobacterium tumefaciens GV3101 carrying pSoup; fruit was agroinjected and leaves were vacuum infiltrated. Input plasmid DNA and transcribed RNA barcodes were sequenced, TPM-normalized, and used to calculate RNA/DNA enhancer activity. Three biological replicates were performed for each assay. DeepTOMATO uses mean enhancer activity across leaf and fruit replicates as the two regression targets.
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 · 12 definitions
element_id
Unique tested tomato promoter-fragment identifier from the deposited data, such as Solyc09g089580-P10.
gene_id
S. lycopersicum gene identifier parsed from element_id, including a transcript version suffix when present.
fragment_number
Sequential 160-bp fragment number parsed from the -P suffix of element_id.
sequence
The 160-bp tomato promoter fragment sequence used in the MPRA.
sequence_length
Sequence length in nucleotides; the package QC requires 160.
leaf_activity
Deposited DeepTOMATO Leaf_activity regression target for the leaf libraries; the paper presents these activity comparisons in log2 activity units and the target is averaged across leaf replicates.
fruit_activity
Deposited DeepTOMATO Fruit_activity regression target for fruit libraries spanning mature-green, breaker, and red-ripe fruit; the target is averaged across fruit replicates.
fruit_minus_leaf_activity
Derived fruit-minus-leaf activity difference, calculated as fruit_activity minus leaf_activity; positive values indicate greater aggregate fruit activity.
fruit_specific_by_published_threshold
Derived TRUE when fruit_activity is greater than 0 and fruit_minus_leaf_activity is greater than 1, applying the paper's stated fruit-specificity threshold to the deposited aggregate targets; FALSE otherwise.
source_split
Original DeepTOMATO data split: train or held-out test.
mpra_active
TRUE because every row is part of the deposited 2,436-row MPRA-active fruit-enhancer dataset.
qc_pass
TRUE after identifier, sequence alphabet/length, finite-value, and duplicate checks.
Quality control
The authors excluded enhancer-barcode associations with fewer than 10 DNA reads, retained RNA barcodes with more than 10 reads in at least one RNA sample, and required at least 10 unique RNA barcodes per sequence for active-enhancer identification. RT-qPCR samples were accepted only when RT-positive and RT-negative reactions differed by at least 8 cycles; three biological replicates showed strong correlation. For this package, rows were additionally required to have a unique identifier, a valid Solyc gene-fragment identifier, exactly 160 A/C/G/T bases, and finite leaf and fruit activity values. All 2,436 source rows passed these checks and were retained.
Curation notes
The publisher version is paywalled, but a public author-uploaded full-text copy was accessible and is represented in full_text.txt. Zenodo provides the matching DeepTOMATO archive and its train/test activity tables; the public NCBI BioProject provides raw DNA/RNA sequencing run metadata but no compact count matrix. Raw sequencing reads were not packaged. Because the deposited model targets aggregate leaf/fruit activities rather than separate mature-green, breaker, and red-ripe tables, this package treats the study as one aggregate tissue-comparison experiment and does not invent stage-specific measurements. No source rows were dropped by package QC.