I am working with Drosophila embryos and I want to sort GFP positive nuclei by FACS, to analyze them by bulk RNA-seq. To nuclei extraction I am following Fly cell atlas protocol. Afterwards I sort 106 nuclei (by BD FACSAria III Cell sorter). The sorted nuclei look fine under the microscope (roundish morphology and not signs of breakage) but, after RNA extraction using TRIZOL there is almost not RNA detectable in my samples. If I repeat the same protocol without FACS sorting, the quality of the RNA looks way better, which makes me think that the nuclei are suffering stress, leading to RNA degradation. Is there anything I can do to prevent such stress?
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