Figure 2
Evaluation of tissue lysis and RNA purification effects on RNA-seq from ethanol-fixed tissue microdissection samples. (a) Workflow of RNA-seq from tissue microdissection samples. The microdissection samples were collected from ethanol-fixed liver tissue using a punching needle. Then, the microdissection samples were lysed by Triton-X100 or Proteinase K, followed by poly(A) RNA purification by oligo (dT) magnetic beads. (TN: Triton-X100, no RNA purification and PP: Proteinase K and RNA purification) The tissue microdissection samples were serially collected from the same mouse liver slice. (b) Electropherograms of cDNA constructed under different tissue processing conditions. (c) The number of protein-coding genes estimated from RNA-seq results. Stars indicate p-value <0.005 determined by Welch’s t-test. (d) Sequencing read proportions assessed by mapping to a reference genome. (e) Comparisons of gene expression levels obtained between fresh tissue bulk RNA and tissue microdissection samples prepared under two different conditions. TPM values were averaged from four samples in the bulk sample pool and eight samples in the microdissection sample pool. (f) Pearson’s correlation coefficients across samples in the dataset including control samples and sample obtained by each method. Box plots show the within-sample range.
