High-resolution transcriptome of human macrophages

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High-resolution transcriptome of human macrophages

  1. 1. High-ResolutionTranscriptomeof HumanMacrophages by Beyer & colleaguesPLOS one 2012Presented byNacho Caballero
  2. 2. CD14+ Monocyte Monocytes follow twopaths of differentiation M1 Macrophage IFNGTNFIRF6 M2 Macrophage IL4 IL13 CSF1 CSF2
  3. 3. Fluorescence Each macrophage subtypeexpresses a unique phenotype % of max cells Mean Fluorescence Units FCGR1A isotype m1 m2 m1 m2 Fluorescence % of max cells Mean Fluorescence Units m1 m2 isotype m1 m2 FCER2
  4. 4. Arrays can discriminatebetween macrophage phenotypes m1 m2 M0
  5. 5. Sequencing and microarraydata are highly correlated 900 308 595  Sequencing Array Log2 FC   Log2 FC  Sequencing Fold Change Array Fold Change
  6. 6. Canonicalmacrophage markers Array Sequencing
  7. 7. (z-scores andheatmaps) Absolute values Z-scores
  8. 8. Canonicalmacrophage markers Array Sequencing
  9. 9. Advantages of sequencing:Detecting alternative splicing PDLIM7 gene  m1 m2 m1 m2 m1 m2 m1 m2 Array mRNA (relative)  Sequencing Isoform 1   Isoform 2   Isoform 4  mRNA (relative)  
  10. 10. Advantages of sequencing:Identifying novel macrophage markers Array Sequencing
  11. 11. Favor gene lists or line charts over z-score heatmaps Sequencing improves resolution andcan answer additional questions Arrays may be good enough toassess gene expression

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