35S enhancer position and orientation library in tobacco leaves
Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco LeavesA barcoded STARR-seq library tested one or two copies of the cauliflower mosaic virus 35S enhancer in forward or reverse orientation at the up, down, up2, and down2 positions of the reporter construct. This table summarizes the public Fig1B_Rep1 plasmid-input and cDNA barcode counts after package QC and aggregates them to construct conditions.
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; 2 d after Agrobacterium infiltration under the normal light/dark growth cycle
Episomal pGreen-derived STARR-seq plasmids were transiently delivered to intact Nicotiana benthamiana leaves by Agrobacterium infiltration. The GFP reporter was driven by a 35S minimal promoter and contained a 15-bp random barcode in the GFP open reading frame; full-length enhancer constructs were represented by approximately 5–10 unique barcodes each. Activity was quantified from matched plasmid-input and reporter-mRNA cDNA barcode counts as the log2 ratio of normalized cDNA to input frequency, with the paper's no-enhancer median normalization also reported.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (18 of 18)
| Row | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||||||
| 2 | ||||||||||||||||||
| 3 | ||||||||||||||||||
| 4 | ||||||||||||||||||
| 5 | ||||||||||||||||||
| 6 | ||||||||||||||||||
| 7 | ||||||||||||||||||
| 8 | ||||||||||||||||||
| 9 | ||||||||||||||||||
| 10 | ||||||||||||||||||
| 11 | ||||||||||||||||||
| 12 | ||||||||||||||||||
| 13 | ||||||||||||||||||
| 14 | ||||||||||||||||||
| 15 | ||||||||||||||||||
| 16 | ||||||||||||||||||
| 17 | ||||||||||||||||||
| 18 | ||||||||||||||||||
| 19 | ||||||||||||||||||
| 20 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 18 definitions
- construct_id
- Unique construct-condition identifier combining enhancer identity, copy number, orientation, and insertion location.
- enhancer_name
- Enhancer identity: 35S for the CaMV 35S enhancer or none for a no-enhancer control.
- enhancer_copy_number
- Number of CaMV 35S enhancer copies in the construct.
- orientation
- Enhancer orientation in the construct: fwd, rev, or NA for no-enhancer controls.
- location
- Author-provided reporter location label: up, down, up2, or down2.
- barcode_count
- Number of linked barcodes passing package QC and aggregated for the construct condition.
- input_count_sum
- Sum of plasmid-input barcode counts across retained barcodes.
- cdna_count_sum
- Sum of recovered reporter-mRNA cDNA barcode counts across retained barcodes.
- log2_enrichment_median
- Median log2(cDNA barcode frequency / input barcode frequency) across retained barcodes.
- log2_enrichment_mean
- Mean log2(cDNA barcode frequency / input barcode frequency) across retained barcodes.
- log2_enrichment_sd
- Sample standard deviation of barcode-level log2 enrichment within the construct condition.
- normalized_log2_enrichment_median
- Median log2 enrichment minus the median enrichment of all joined no-enhancer control barcodes, matching the paper's normalization.
- source_replicate
- Source count-file replicate label.
- replicates_available
- Number of source biological replicates represented in this packaged table.
- replicates_in_paper
- Number of biological replicates reported for this experiment in the paper.
- source_subassembly
- Relative path to the barcode-to-construct subassembly file used for joining.
- source_input_count_file
- Relative path to the plasmid-input barcode count file used.
- source_cdna_count_file
- Relative path to the reporter-mRNA cDNA barcode count file used.
Quality control
The authors filtered barcode counts below 5 and, for the complete study analysis, discarded barcodes present in only one of three biological replicates. Their reported replicate-quality criteria were Spearman correlation of at least 0.6 for individual barcodes and at least 0.7 for aggregated fragments or variants. For this package, the only compact count files released with the analysis repository are Fig1B_Rep1 input and cDNA counts, so the across-replicate presence filter cannot be applied; retained entries instead have a linked subassembly record and both input and cDNA counts of at least 5. Counts were normalized over the joined mapped barcode set, following the authors' analysis script.
Curation notes
The paper performed three biological replicates, but the linked repository exposes compact count outputs for Fig1B Rep1 only; the complete 84-run sequencing release remains available through BioProject PRJNA627258 and is represented by run metadata in raw_data. The raw repository includes subassembly maps for additional figures, but no compact activity matrices for them. This package therefore presents a reproducible single-replicate construct-level view rather than an inferred complete-study summary. The no-enhancer records retain the authors' placeholder location labels.