Finding RNA-Seq datasets across species

[Thias]

Good place to start: GEO datasets

You can use nested search queries to narrow down the results to relevant studies. This very general one e.g. lists RNAseq studies from Mouse:

"Mus musculus"[porgn] AND "Expression profiling by high throughput sequencing"[Filter]

[alittleboy]

I plan to examine several RNA-Seq datasets (say 5-6), and hopefully there have the following characteristics:

1. Different species: human, mouse, zebrafish, yeast, arabidopsis, etc.
2. With different experimental designs: two-group comparison, batch effects, time series, etc.
3. Different sequencing platforms.
4. Studied and published in either biological or statistical papers.

Because I will be focusing on the statistical evaluations, the datasets are preferred to be in the form of read counts table (summarized at the gene-level), with meta-data information. However, it is okay that only raw data are available.

Please share your thoughts on obtaining such datasets from online RNA-Seq repositories/databases. If you know some paper that include comprehensive evaluations on statistical methods applied to real RNA-Seq data, please let me know

Thank you so much!