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Chunk #26 — Methods — Microfluidic qPCR (pooled cell samples)

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Neurotoxic reactive astrocytes are induced by activated microglia.
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Total RNA was extracted from immunopanned cells using the RNeasy Plus kit (Qiagen) and cDNA synthesis performed using the SuperScript® VILO cDNA Synthesis Kit (Invitrogen, Grand Island, NY, USA) according to supplier protocols. We designed primers using NCBI primer blast software (http://www.ncbi.nlm.nih.gov/tools/primer-blast/) and selected primer pairs with least probability of amplifying nonspecific products as predicted by NCBI primer blast. All primers had 90–105% efficiency. We designed primer pairs to amplify products that span exon–exon junctions to avoid amplification of genomic DNA. We tested the specificity of the primer pairs by PCR with rat and mouse whole-brain cDNA (prepared fresh), and examined PCR products by agarose gel electrophoresis. For microfluidic qRT-PCR, 1.25 μl of each cDNA sample was pre-amplified using 2.5 μl of 2× Taqman pre-amplification master mix (Applied Biosystems, Waltham, MA, USA) and 1.25 μl of the primer pool (0.2 pmol each primer/μl, primer sequences for rat and mouse are provided in Supplemental Data Tables 1–2). Pre-amplification was performed using a 10 min 95 °C denaturation step and 14 cycles of 15 s at 95 °C and 4 min at