BaseSearch-designed synthetic maize STEs in a 35S minimal-promoter STEM-seq screen
From Natural Discovery to AI‐Guided Design: A Curated Collection of Compact Enhancers for Crop EngineeringA 60-bp AI-designed synthetic enhancer library was tested in maize protoplasts with the pSTEM02 35S minimal-promoter STEM-seq reporter. The table contains the measured synthetic records provided in Supplementary Sheet 11, including BaseSearch predictions and two-replicate activity values.
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
Basal / Untreated
The same custom STEM-seq plasmid MPRA configuration was used for BaseSearch-designed 60-bp sequences in maize protoplasts: three barcodes per candidate, intron-separated reporter cDNA/input-plasmid measurements, and two biological replicates. The paper states that 5000 candidates were stratified by predicted activity and screened with 500 inactive natural controls; Supplementary Sheet 11 supplies 1094 measured synthetic records and does not include raw barcode counts or the full 5000-candidate negative set.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 9 definitions
- source_record_id
- Unique processed row identifier; equals the source element ID except when the source repeats an accession, where a source-record suffix disambiguates the repeated measurements.
- element_id
- Unique synthetic STE accession identifier.
- sequence
- Tested AI-designed 60-bp sequence in the 5-prime to 3-prime orientation.
- sequence_length_bp
- Sequence length in base pairs after sequence QC.
- predicted_activity
- BaseSearch predicted activity score used to stratify/design the synthetic candidate.
- activity_repeat1
- STEM-seq enhancer activity for biological replicate 1 (fold change).
- activity_repeat2
- STEM-seq enhancer activity for biological replicate 2 (fold change).
- activity_mean
- Mean STEM-seq enhancer activity across the two biological replicates (fold change).
- activity_status
- Derived from the paper’s screening definition: active when mean activity is greater than 1.0-fold.
Quality control
The source table provides predicted scores, 60-bp sequences, and two replicate STEM-seq activity values. Package-level QC retained only records with a non-empty synthetic ID, a canonical 60-bp A/C/G/T sequence, and finite predicted, replicate, and mean activity values. Of 1094 source records, 1094 passed and 0 were omitted. All retained records have mean activity >1.0-fold (1094/1094), matching the paper’s active-screen definition; no element-level P-value/FDR fields are supplied for this sheet.
Curation notes
The source is raw_data/ADVS-13-e16600-s007.xlsx, Supplementary Sheet 11. It is a measured STEM-seq screen, not merely the in-silico BaseSearch candidate list in Sheet 10 and not the separate dual-luciferase validation of the top ten designs. The paper reports 455 functional elements among 5000 screened synthetic candidates; the available Sheet 11 contains a smaller post-screen measured subset, so this table should not be interpreted as the complete candidate library.