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High-resolution transcriptome of human macrophages
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High-resolution transcriptome of human macrophages

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Journal club presentation

Published in Technology
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Transcript

  • 1. High-ResolutionTranscriptomeof HumanMacrophages by Beyer & colleaguesPLOS one 2012Presented byNacho Caballero
  • 2. CD14+ Monocyte Monocytes follow twopaths of differentiation M1 Macrophage IFNGTNFIRF6 M2 Macrophage IL4 IL13 CSF1 CSF2
  • 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. Arrays can discriminatebetween macrophage phenotypes m1 m2 M0
  • 5. Sequencing and microarraydata are highly correlated 900 308 595  Sequencing Array Log2 FC   Log2 FC  Sequencing Fold Change Array Fold Change
  • 6. Canonicalmacrophage markers Array Sequencing
  • 7. (z-scores andheatmaps) Absolute values Z-scores
  • 8. Canonicalmacrophage markers Array Sequencing
  • 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. Advantages of sequencing:Identifying novel macrophage markers Array Sequencing
  • 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