Supplementary Figure 7: RNA SPOTs has little bias in GC content and transcript length. | Nature Methods

Supplementary Figure 7: RNA SPOTs has little bias in GC content and transcript length.

From: Profiling the transcriptome with RNA SPOTs

Supplementary Figure 7

(a) Hexbin plot of NIH/3T3 mean SPM (n=2) shows no obvious trend with transcript GC content. (b) Transcript length does not bias RNA SPOTs detection. (c) Same as (a) but for genes with < 1 FPKM. (d) same as (b) but for genes with < 1 FPKM. (e) Boxplots of different groups of genes with different expression levels against transcript GC content. n = 1360, 2323, 1473, 2645 for each group from left to right. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers. (f) Boxplot of SPM against transcript length. (g) Replicate plot of SPOTs as shown in Fig 2b. (h) Simulated replicates with Poisson noise. The total number of simulated SPOTs (n1=447,094, n2=448,249) was set to match the experimental replicates. (i). SPOTs data from two sets of field of views (FOVs) from the E14 experiment 3, x-axis contains 25 FOVs (n1=269,459 spots), y-axis contains another 25 FOVs (n2=295,403 spots).

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