Data for: "Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome"

Description of the data and file structure

This is the supplementary data for the paper titled "Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.


File: Data_artemia_single_nucleus_atlas.zip

Description: 

The compressed archive contains the following three folders (Each folder contains a README.md file describing its content):

Genome annotation
Annotation used and reciprocal best hits to the published Artemia franciscana annotation (Bett et al., 2024) and reciprocal best hits to Drosophila genes.


Seurat objects
Seurat objects: Expression Seurat object (all replicates), Expression and ATAC Seurat object (replicates 3 and 4). The Velocyto_output folder includes the loom files generated by Velocyto.


Modules and GO enrichment
Includes the modules from the networks analysis using hdWCGNA and the GO enrichment results from https://string-db.org/


Code/software to view the data:

Seurat 4.4.0

R 4.3.3

python 3.9


Other publicly accessible locations of related data:

The raw data is available on NCBI bioproject PRJNA1128544

The single-nucleus atlas is hosted on the UCSC cell browser website and can be accessed using the following link: https://brine-shrimp-repro.cells.ucsc.edu

The code used for the analysis is available on GitHub using the following link: https://github.com/Melkrewi/Artemia-snRNAseq-Project.git