STARR-seq screen for candidate A. coluzzii enhancers
Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzziiA pooled genomic-fragment STARR-seq library from 60 wild A. coluzzii was transfected into A. coluzzii 4a3A cells in three biological replicates. Candidate enhancers were selected near six vector-biology genes where reporter cDNA coverage visibly exceeded the plasmid-DNA baseline.
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; 24 h after library transfection
Episomal pSTARR-seq_fly reporter; RNA-derived cDNA and plasmid-DNA input were sequenced on Illumina HiSeq 2500 in 2 × 125 bp mode. The original paper selected candidates by visual IGV comparison rather than a published per-element count/statistical table.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (14 of 14)
| Row | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||
| 2 | ||||||||||||||
| 3 | ||||||||||||||
| 4 | ||||||||||||||
| 5 | ||||||||||||||
| 6 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 14 definitions
- element_id
- Short element identifier used by the paper and FASTA supplements.
- proximal_gene
- Nearest annotated gene used to name the candidate enhancer; proximity is not proof of target-gene regulation.
- gene_id
- Anopheles gambiae/coluzzii gene identifier reported by the paper.
- chromosome
- Chromosome arm in the PEST AgamP4 coordinate system.
- start
- 1-based inclusive enhancer interval start from Table 1.
- end
- 1-based inclusive enhancer interval end from Table 1.
- interval_length_bp
- Inclusive interval length calculated as end minus start plus one.
- library_context
- Source pooled genomic-fragment library and cloning context.
- starr_screen_evidence
- Published qualitative evidence used for candidate selection: cDNA reporter-track coverage exceeded plasmid-DNA baseline.
- replicate_count
- Number of biological STARR-seq replicates reported by the paper.
- activity_call
- Paper-level candidate activity call; no numeric enrichment was published for these six manually inspected intervals.
- ena_study_accession
- ENA study accession for the underlying short-read files; FASTQ files are not copied into this package.
- source_figure
- Publication figure/table supporting the row.
- qc_pass
- All six published candidate calls passed the paper’s cDNA-versus-plasmid screen and three-replicate review; DLX negative control was omitted from this active-element table.
Quality control
Retained only the six intervals explicitly called as candidates in the paper after visual comparison of cDNA and plasmid tracks across three biological replicates. The DLX interval was a negative control and is intentionally excluded from the active-element table.
Curation notes
ENA provides the underlying cDNA/plasmid short reads under PRJEB34434; the package includes the run manifest but not the multi-gigabyte FASTQ files. The paper does not publish numeric per-element STARR-seq scores for the six manually selected intervals.