DOI: 10.5061/dryad.q573n5twb
title: Seurat objects for the manuscript Single-cell consequences of X-linked meiotic drive in stalk-eyed flies

description: 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.
description: # 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 &gt; 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 &gt; 200 and mitochondrial
 expression &lt; 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 ## Access information Related
 datasets: https://doi.org/10.5061/dryad.ht76hdrtj
 https://doi.org/10.5061/dryad.zkh1893kb
 https://doi.org/10.5061/dryad.j6q573nqw
 https://doi.org/10.5061/dryad.brv15dvk3