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I am wondering how much total RNA could be extracted from a single D. melanogaster brain. I could not find this information from the literature.

The closest hit was this paper, that claims that 16-21.9µg of total RNA can be extracted from 100 brains, which translates to at least 160ng for a single brain.

I also found in the supplementary material of this paper that 1µg of total RNA was extracted from 5-10 fly brains, which would also make > 100ng for a single brain.

I am asking the question because I am envisioning to perform RNA-seq of single Drosophila brains. The standard Illumina TruSeq library preparation protocol works with 100ng of total RNA. Thus I am wondering if this is realistic, or if I should rather target low input library preparation protocols.

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In my opinion you should try low input library prep protocols because in my experience even with a decent quantity of RNA, standardizing the sequencing is not an easy job. The manual says that this kit works with 10-20ng of RNA; always assume the higher limit to be true. There is a higher chance of loss (relative) during extraction also. Try doing precipitation with 5M LiCl and a little glycogen along with alcohol; but assuming your yield is 80ng you can still run replicates for statistical comparisons.

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