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    Nicolas Bray said:

    Quake’s response “Our single cell RNAseq experiments included all 91 of the “live” single cells and 1 of the “dead” single cells” flatly contradicts his own paper, where we find (among other statements):

    “We made a total of 102 single-cell RNA-seq libraries using two tube-based methods (6 libraries) and one microfluidic method (96 libraries):”

    “the results are averaged over all 96 chambers in the C1 chip.”

    “reads obtained from the 96 single-cell transcriptomes”

    I’d also point out that Quake’s statement “In our own analyses C09 and the other controls were excluded from the single cell data.” is in direct contradiction with the second quote above.