Seurat objects for the manuscript Single-cell consequences of X-linked meiotic drive in stalk-eyed flies

This dataset contains R seurat objects used to reproduce the single-cell RNA-seq analyses for the manuscript Single-cell consequences of X-linked meiotic drive in stalk-eyed flies. Testis tissue from eight male Teleopsis dalmanni (drive and standard genotypes) was dissociated and sequenced using the 10X Genomics Chromium platform. Sequencing reads were processed with Cell Ranger v7.2.0, and downstream filtering, doublet removal, integration, and clustering were performed in Seurat v5.1.0. The final dataset (seurat_final.RData) comprises 12,217 high-quality cells expressing 12,454 genes, with cell types identified using orthologous markers from Drosophila melanogaster. Provided files include the filtered integrated Seurat object and a final processed object with reclustered and annotated cell types. These resources enable full reproducibility of the analyses and support future exploration of testis cell populations in stalk-eyed flies.
, , # Seurat objects for the manuscript Single-cell consequences of X-linked meiotic drive in stalk-eyed flies

Dataset DOI: [10.5061/dryad.q573n5twb](10.5061/dryad.q573n5twb)

## Description of the data and file structure

Sequencing data from Price et al. (2025; 10.5061/dryad.zkh1893kb) was processed using Cell Ranger v7.2.0. First, a custom reference genome was built with the *T. dalmanni reference genome using mkref. Using cellrangers count function, fastq reads were then aligned against the custom index and counted, creating gene-by-cell count matrices. Data filtering and downstream analyses were performed using Seurat v5.1.0 in R v4.3.2.* Cells in each sample were removed from the analysis if they expressed fewer than 200 features and more than 20% mitochondrial expression. Count data for each sample was also filtered by only keeping genes with expression (counts > 1) in at least three cells. We used DoubletFinder v2.0.4 in R with default parameters to identify and remove doublets. O...,