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Publicly available RNA-seq data of dopaminergic neurons

Hi all, I am after some RNA-seq data on dopaminergic neurons from human, not from human cell lines. How and where should I go and download these datasets? What software or tools will allow comparison of differential gene expression and days of post-differentiation of the dopaminergic neurons? For instance, suggestions to any web tool that allows searching of gene name(s) and days of post-differentiation against a given RNA-seq dataset would be great too. Your help is much appreciated!

genome rna-seq

1 answer

If there are any publicly available datasets then you can find them via GEO and/or SRA/ENA. It looks like the available datasets are ES-cell derived, so if you want sequence from primary microdissected dopaminergic neurons then you're likely out of luck. I should note that this is unsurprising, since it's kind of sketchy to try and get a neuron out of the brain intact without changing its properties.

For the actual analysis, you'll usually download the raw fastq files, so you'll need to trim the files, align them, get counts, and perform statistics yourself. You can use Galaxy to do all of this if you're unfamiliar with using the command line.

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