Genome-wide S2 STARR-seq enhancer activity across five Drosophila species
Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolutionGenomic DNA from D. melanogaster, D. yakuba, D. ananassae, D. pseudoobscura, and D. willistoni was screened in the same D. melanogaster S2 cell trans-regulatory environment. The table contains the study's combined two-biological-replicate enhancer peak calls after translation to dm3-compatible coordinates.
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
Episomal self-transcribing enhancer assay using randomly sheared genomic fragments cloned downstream of a minimal promoter. Paired-end STARR-seq cDNA and input reads were mapped to each source-species assembly, PCR/redundancy-filtered, and species-specific fragments were lifted to the dm3 coordinate system; enhancer activity is reported as cDNA/input enrichment at the peak summit.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (12 of 12)
| Row | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||
| 2 | ||||||||||||
| 3 | ||||||||||||
| 4 | ||||||||||||
| 5 | ||||||||||||
| 6 | ||||||||||||
| 7 | ||||||||||||
| 8 | ||||||||||||
| 9 | ||||||||||||
| 10 | ||||||||||||
| 11 | ||||||||||||
| 12 | ||||||||||||
| 13 | ||||||||||||
| 14 | ||||||||||||
| 15 | ||||||||||||
| 16 | ||||||||||||
| 17 | ||||||||||||
| 18 | ||||||||||||
| 19 | ||||||||||||
| 20 | ||||||||||||
| 21 | ||||||||||||
| 22 | ||||||||||||
| 23 | ||||||||||||
| 24 | ||||||||||||
| 25 | ||||||||||||
| 26 | ||||||||||||
| 27 | ||||||||||||
| 28 | ||||||||||||
| 29 | ||||||||||||
| 30 | ||||||||||||
| 31 | ||||||||||||
| 32 | ||||||||||||
| 33 | ||||||||||||
| 34 | ||||||||||||
| 35 | ||||||||||||
| 36 | ||||||||||||
| 37 | ||||||||||||
| 38 | ||||||||||||
| 39 | ||||||||||||
| 40 | ||||||||||||
| 41 | ||||||||||||
| 42 | ||||||||||||
| 43 | ||||||||||||
| 44 | ||||||||||||
| 45 | ||||||||||||
| 46 | ||||||||||||
| 47 | ||||||||||||
| 48 | ||||||||||||
| 49 | ||||||||||||
| 50 |
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 row identifier derived from cell type, species code, and source peak rank.
- cell_type
- STARR-seq assay context; S2 for Schneider 2 cells.
- species
- Drosophila species from which the genomic DNA/library fragments were sourced.
- species_code
- Study shorthand for the source species (Dmel, Dyak, Dana, Dpse, or Dwil).
- reference_genome
- Common coordinate system used for the table after species-specific fragments were lifted to dm3.
- chromosome
- Chromosome name in the dm3-compatible coordinate system.
- summit_position
- STARR-seq peak summit coordinate reported by the source peak file.
- enrichment_over_input
- Fold enrichment of STARR-seq cDNA fragment density over input at the peak summit.
- p_value
- Peak-call P value reported by the study.
- peak_call_set
- Peak call generated from the combined biological replicates.
- source_peak_file
- Path of the source combined peak file within Supplementary_Data_Set_1.zip.
- source_peak_rank
- 1-based row order of the peak in its source combined peak file.
Quality control
The study trimmed paired-end reads to 36 bp, mapped them with Bowtie to droYak2, droAna3, dp4, droWil1, or dm3, collapsed PCR duplicates by identical fragment coordinates/strand, applied an additional redundancy filter for clustered sequence artifacts, and retained uniquely liftable fragments whose lifted length was 10–200% of the original. Peaks were called at enrichment >=3-fold over input and P <=0.001 (reported FDR <0.1%); two independent biological replicates were reported as highly reproducible (PCC >0.9). The processed table retains only rows from the combined peak-call files meeting those study thresholds; no source peak rows were removed.
Curation notes
D. melanogaster data were reused from the earlier genome-wide STARR-seq screen, while the other four species were screened in this study. The downloadable combined files contain 2,325 Dmel, 2,293 Dyak, 2,093 Dana, 3,461 Dpse, and 2,860 Dwil rows; the paper's Supplementary Table 1 reports 2,325, 2,293, 2,096, 3,469, and 2,860, respectively. The table preserves the downloadable file contents and uses the reported dm3-compatible coordinates; the generic Schneider 2 Cellosaurus entry is used because the exact S2 isolate was not specified.