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

Published Aug 27, 2025 on Dryad. https://doi.org/10.5061/dryad.q573n5twb

Data files

Aug 27, 2025 version files 2.62 GB

integrated_seurat_nf200_mtr0.20_gu0_newref_Seurat5.1_df0.08.RData

1.48 GB
README.md

2.39 KB
seurat_final.RData

1.14 GB

Abstract

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.

Dataset DOI: 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. Our dataset may contain some cells with multiple nuclei because they have yet to fully complete cell individualisation post meiosis at the point we dissected the testes; however, we expect the nuclei in these multinucleated cells to produce similar transcriptomes, and so we do not expect this to bias our results.

The filtered dataset consisted of 12,217 cells across the eight samples, expressing 12,454 genes, with 7,608 cells from drive individuals and 4,609 cells from standard individuals. Seurat objects from all eight samples were then integrated post-filtering using the ‘SCTransform’ function.

Files and variables

File: integrated_seurat_nf200_mtr0.20_gu0_newref_Seurat5.1_df0.08.RData

Description: Dataset filtered for nFeatures > 200 and mitochondrial expression < 20%. This data is not yet filtered for unknown cell types or cell types under-represented across samples.

File: seurat_final.RData

Description: Processed dataset filtered for unknown cell types and reclustered. Cell types were then annotated using established Drosophila markers for the testes cell types.

Code/software

Seurat v5.1.0

R v4.3.2

DoubletFinder v2.0.6