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. Author manuscript; available in PMC: 2018 Apr 12.
Published in final edited form as: Dev Biol. 2016 Jul 26;426(2):360–373. doi: 10.1016/j.ydbio.2016.06.003

Figure 2. RNA-Seq read alignment and analysis.

Figure 2

(A) Proportion of RNA-Seq reads that were mapped to the Xenopus laevis 9.1 genome assembly across experimental naïve (-), contralateral control (c) and crush (x) samples demonstrates good mapping rates across the various days post-crush (Dpc). (B) Read counts, expressed as FPKM, for each gene sequenced in the crushed (FPKMC; x-axis) versus control eye (FPKMX; y-axis) showing both up- and down-regulation in the days following injury. (C) Comparison of changes in gene expression following optic nerve crush between homeolog-pairs (L x-axis, S y-axis) across the post-injury time course, shows overall correlation between pairs with clear outliers. (D) The magnitude of difference between changes in gene express among homeolog-pairs, quantified by Euclidean distance, increases over time after optic nerve injury.