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How do you obtain specific mRNA transcript levels for comparison from a Hi-Seq dataset?

I have HiSeq data from mice exposed to two conditions. I would like to answer the following question: "Is there a significant difference in mRNA transcript levels when comparing condition A to ...
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how to make plasma cells adhere to the bottom of a microplate?

I am isolating single plasma cells by FACS sorting into 384-well plates, with the intent to assay the supernatant and clone H/L chains from positive wells. The efficiency of the PCR is however low, ...