SB versus Sb haplotype STARR-seq enhancer activity in Drosophila S2 cells
The Fire Ant Social Chromosome Exerts a Major Influence on Genome RegulationRandomly sheared 400–750 bp genomic DNA from pooled S. invicta males carrying SB or Sb was cloned into pSTARR-seq_fly and transfected into D. melanogaster S2 cells. Three independent flasks per genotype generated paired plasmid-DNA input and plasmid-derived mRNA STARR-seq libraries; the processed table contains the study's peak-level enhancer activity summary.
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 pSTARR-seq_fly reporter (Addgene #71499) with a synthetic intron used for junction PCR enrichment of plasmid-derived mRNA. Genomic DNA was pooled from 9 SB males and 10 Sb males, sonicated, size-selected at 400–750 bp, and cloned as one library per genotype. Three replicate flasks were transfected per genotype with 12 µg library DNA and harvested after 48 h; each flask yielded a DNA-input library and an mRNA STARR library. Libraries were sequenced as 2 × 50 bp paired-end reads on a NovaSeq SP. The table's Sb_enh_strength and SB_enh_strength are study-reported log2 enhancer strengths from normalized STARR mRNA relative to DNA input; the genotype-by-library interaction effect is the reported Sb-versus-SB differential activity statistic.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (19 of 19)
| 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 · 19 definitions
- element_id
- Unique processed element identifier in the form chromosome:start-end, using the source chromosome label and reported peak coordinates.
- chromosome
- Chromosome label from Table S13; 'unplaced' denotes unplaced scaffolds.
- chromosome_accession
- Reference sequence accession from the source table, such as NC_052664.1 or an unplaced NW_ accession.
- start
- Reported start coordinate of the merged STARR-seq peak.
- end
- Reported end coordinate of the merged STARR-seq peak.
- peak_id
- Peak identifier parsed from the source Parent=peak label.
- Sb_activity_log2
- Study-reported log2 enhancer strength for the Sb genotype pool, based on normalized STARR mRNA relative to DNA input.
- SB_activity_log2
- Study-reported log2 enhancer strength for the SB genotype pool, based on normalized STARR mRNA relative to DNA input.
- Sb_active
- Source enhancer call for the Sb pool: yes/no.
- SB_active
- Source enhancer call for the SB pool: yes/no.
- Sb_vs_SB_interaction_log2
- Reported genotype-by-library interaction effect for Sb versus SB activity; positive values indicate higher activity for Sb.
- Sb_vs_SB_interaction_qvalue
- q-value for the reported Sb-versus-SB genotype-by-library interaction.
- activity_bias
- Source direction call for the interaction: Sb, SB, or not_significant.
- priority_feature
- Highest-priority RefSeq genomic feature overlapping the peak, using the paper's annotation order.
- priority_gene
- Nearest/priority-assigned RefSeq gene identifier; blank indicates source NA/no assignment.
- all_genes
- All RefSeq genes within the source annotation window; blank indicates none reported.
- priority_gene_annotation
- RefSeq annotation for the priority gene; blank indicates source NA/no annotation.
- within_supergene
- Whether the peak falls within the social-chromosome supergene region according to the source table.
- source_supplementary_table
- Supplementary-table provenance for the processed record; all rows are from Table S13.
Quality control
The authors trimmed low-quality bases and adapter contamination with fastp using default parameters, aligned reads to GCF_016802725.1 with bwa mem, and sorted alignments with SAMtools. MACS2 called peaks separately for each of the six replicate flasks using the paired DNA input as control (-f BAMPE, -g 3.8e8, --keep-dup all, -q 0.05); the six peak sets were merged into 67,105 candidate regions. featureCounts quantified all input and STARR libraries, and limma/edgeR modeled enhancer activity as genotype plus librarytype:genotype. The study retained 23,616 peaks with significant positive enhancer activity in one or both genotypes; genotype-biased enhancers were tested with the genotype × library-type interaction and qvalue < 0.05. Package QC additionally required nonmissing finite coordinates, finite activity/effect/q-value fields, q-values in [0,1], and unique element coordinates. All 23,616 source records passed these checks; 0 records were excluded.
Curation notes
This is one paired-genotype STARR-seq experiment, not separate experiments for SB and Sb. Table S13 is a published peak-level summary of 23,616 significant enhancer regions; it does not expose the underlying replicate-level featureCounts matrix, per-barcode counts, or insert sequences. The source library information in Table S18 lists one SB DNA source (BigB-2; 9 whole males) and one Sb DNA source (littleb-1; 10 whole males), six flasks total, and paired DNA-input/mRNA libraries. Raw sequencing reads are available under PRJNA1071646 but were not downloaded, consistent with the package instruction to omit bulky raw read files.