RNA-Seq Data on Osmoregulation in Three Heteromyid Rodent Species

Featuring RNA-seq data from kidney tissue of three Heteromyid rodent species, used to study the genetic basis of water retention. The analysis identified 1,890 differentially expressed genes between arid and mesic species and 323 annotated full-length genic regions. It was authored by Nicholas J. Marra and published in 2020.

Use Cases

• Identify differentially expressed genes between desert-adapted and mesic rodent species using the 1,890 DE genes identified.
• Conduct selection tests on putative orthologues, such as the 6 genes showing evidence of positive selection (dn/ds >1).
• Perform a reciprocal BLAST analysis on the 3,511 sets of putative orthologues to study gene evolution across species.
• Compare annotated genic regions, including the 323 full-length sequences, to known Mus musculus references for functional annotation.

Strengths

• Analysis is based on RNA-seq data from three species across three subfamilies, providing a phylogenetic control.
• Identified 1,890 genes with consistent differential expression patterns between arid and mesic species.
• Reciprocal BLAST analysis revealed 3,511 sets of putative orthologues and 323 annotated full-length genic regions.

Limitations

• The dataset is derived from only three species, limiting broad phylogenetic inferences.
• Sample data and raw file formats are unavailable, hindering direct re-analysis of sequence reads.
• The specific number of biological replicates per species is not stated, which could affect statistical power.

Provenance

Source

Dryad digital repository.

Collection Method

RNA sequencing of kidney tissue from Dipodomys spectabilis, Chaetodipus baileyi, and Heteromys desmarestianus.

Freshness

Data was last updated in 2020.

Geography

Species sampled from temperate desert and tropical mesic habitats.