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  • Finding RNA-Seq datasets across species

    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!

  • #2
    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:

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

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