1. RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration 
Henning Onsbring, Mahwash Jamy, Thijs J.G. Ettema 
Current Biology 
Volume 28, Issue 8, Pages e3 (April 2018)
DOI: /j.cub
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2. Figure 1
Overview of Experimental Design, Cell Morphology, and Clustering of Differential Expression Data
(A) cDNA was generated from single-cell fragments. Eight different conditions were included in the experiment, corresponding to fragments regenerating until four different time points post-split. Both anterior and posterior parts of the cell were analyzed.
(B) Photos of regenerating cell fragments at the different time points. Both scale bars represent 200 μm.
(C) Principal-component analysis (PCA) based on the expression level of all genes for each replicate included in the experiment.
See also Table S2.
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3. Figure 2 Intersection Size among All Conditions
The highest number of upregulated genes were found in P300, followed by P180 and P90. The most common regulation pattern for differentially expressed genes was to be upregulated at P90, P180, and P300.
See also Figure S1 and Tables S3 and S4.
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4. Figure 3 Heatmap with Conditions and Genes Hierarchically Clustered
Clustering of both genes and conditions is based on expression patterns. On the heatmap, red indicates high- and blue indicates low-expression level of the genes. The significantly enriched biological processes for each gene cluster are shown in the side panel. Red and blue backgrounds are given to up- and downregulated processes, respectively. When Stentor is wounded, the concentration of ions in the cell changes due to damage in the cell membrane. After Stentor has sealed the wound, it is expected that ion transport is needed to re-establish the ion concentration gradients over the membrane. This can also be seen in the heatmap where the cluster with enriched ion transport contains a lot of genes with higher expression levels at 10 min compared to the control. NRC, non-regenerating cells; A, anterior; P, posterior.
See also Figure S2, Table S1, and Mendeley Data.
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5. Figure 4 Expression Patterns for Ccr4-Not Subunits
The expression profiles of five Not4 paralogs, marked with red lines, deviate from the expression patterns of the other subunits.
See also Figure S3.
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