Fig. 7.

Concordance of expression quantification and DEG detection using the SMARTer Ultra Low RNA Kit. For the purpose of evaluation, the libraries prepared from the same biological conditions with the TruSeq Stranded mRNA protocol are also included. a Smoothed color density representation scatter plots (top, right) and Spearman’s rank correlation coefficients (bottom left) for all library pairs using log₂(cpm + 1) values. 100 and 1000 represent the SMARTer Ultra Low RNA Kit using 100 and 1000 cells. b Principal component analysis (PCA) of all libraries using log₂(cpm + 1) values. Red, blue, and green represent libraries prepared with the ultra-low protocol 100 cells, ultra-low protocol 1000 cells, and TruSeq Stranded mRNA protocol, respectively. Circles and triangles represent control and experimental libraries, respectively. c Venn diagram showing the number of DEGs recovered with the SMARTer Ultra Low RNA (100 cells and 1000 cells) and the TruSeq Stranded mRNA kits. d Pairwise scatter plots of log₂ ratio values between the biological conditions using the DEGs. The black dots represent genes called as differentially expressed in libraries prepared with both kits, and the colored dots represent genes called as differentially expressed in libraries from only one kit. The Spearman’s rank correlation coefficient is shown at the top of each plot. The Venn diagram to the left of each scatter plot shows the number of DEGs called for the data produced using both or only one of the protocols