README

Method

Sample collection:

• Snap frozen PDX tumor tissue

  Sample List

RNA extraction:

• Allprep DNA/RNA Mini Kit (Cat. 80204 QIAGEN)

RNA Sequencing Kit/Platform

• Illumina TruSeq Standard Total RNA Kit with RiboZero Plus
• ~50 million reads per sample
• Novaseq

Analysis

• Samples from pt21A1 were excluded from most analysis due to

• Applied “Xengsort” package on FASTQ files, split raw FASTQ files into human and mouse reads, data saved in separate folder.

  • Host (20210927 Host Analysis)
  • Graft (20210927 Host Analysis)

• Host analysis: (folder name: 20220109analysis, please ignore other folders)

  PCA plot

  DESeq2 LRT analysis

  • Top 1000 ranked genes from LRT analysis were further select for GSEA analysis
  • Result sheet format:
    • Patient meta data
    • Raw counts
    • Normalized count
    • Variance stabilized count
    • LRT ranked genes with differential expression statistic
    • top 1000 LRT ranked gene Hallmark Gene Set Enrichment Analysis

• Graft analysis: (folder name: 20220109analysis)

  PCA plot

  DESeq2 LRT analysis

  • Gene Set Enrichment Analysis from top 1000 ranked genes from LRT analysis
  • Gene Set Variance Analysis from top 1000 ranked genes from LRT analysis
  • Result sheet format:
    • Patient meta data
    • Raw counts
    • Normalized count
    • Variance stabilized count
    • LRT ranked genes with differential expression statistic
    • top 1000 LRT ranked gene Hallmark Gene Set Enrichment Analysis