scRNA-seq

single-cell RNA-seq basic data

• PCA result
  
• tSNE result
  
• Marker gene expression in PCA
  
• Marker gene expression in tSNE
  

single-cell RNA-seq pseudotime analysis

• niPSCs Monocle method
• R204W Monocle method
• R304W Monocle method
• All samples Monocle method
• Monocle method
  
• Diddusion Maps method
  
• Slicer method
  
• TSCAN method
  

single-cell RNA-seq and public bulk RNA-seq correlation

• Correlation in PCA
  
• PCA split with different cell type
  
• Correlation in tSNE
  
• tSNE split with different cell type
  

---

bkRNA-seq

bulk RNA-seq basic data

xlsx files

• All samples Deseq2 result summary
  
• Deseq2 differental expression gene results
  
• Go analysis result
  I use clusterProfiler R package to do GO analysis with GO over-representation test method.
• All samples expression results(RPKM and TPM)
  
RPKM=log(2,(reads*10e6)/(geneLength*allReads)+1)
rate=counts/lengths
TPM=log(2,rate/sum(rate)*1e6+1)


pdf files

• No KRT Cluster
  
• All sample Cluster
  

no KRT bulk RNA-seq data

• PCA genelist (New Data!)
• Cluster genelist (New Data!)
• Cluster each clusters Go analysis results (New Data!)
• PCA each PCs Go analysis results (New Data!)

bulk RNA-seq and single-cell RNA-seq correlation

• Correlation in PCA
  
• Correlation in tSNE
  

normal iPSCs and normal KC bulk RNA-seq data

xlsx files

• PCA genelist
  
• Cluster genelist
  
• Cluster each clusters Go analysis results
  
• PCA each PCs Go analysis results
  

pdf files

• Nnormal bkRNA cluster and PCA result
  
• Nnormal bkRNA cluster gene expression
  

normal iPSCs and normal KC no C2 bulk RNA-seq data

xlsx files

• PCA genelist (New Data!)
• Cluster genelist (New Data!)
• Cluster each clusters Go analysis results (New Data!)
• PCA each PCs Go analysis results (New Data!)

pdf files

• Nnormal bkRNA cluster and PCA result (New Data!)
• Nnormal bkRNA cluster gene expression (New Data!)