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Lab meeting 25/9

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Nacho Caballero
Nacho Caballero

This document discusses detecting viral infections using microarrays. It shows microarray data that can distinguish gene expression profiles between uninfected cells and cells infected with the Lassa or Marburg viruses over time. Sensitivity and specificity metrics are calculated to evaluate how well the microarrays can identify Lassa versus Marburg infections. The next steps discussed are to use updated microarray platforms and RNA sequencing to better distinguish between the viruses and identify non-coding RNA expression.

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Detecting Viral Infections Using Microarrays Nacho Caballero Connor Lab Wednesday, September 26, 12
RIG-I Lassa Wednesday, September 26, 12
RIG-I uninfected Lassa Wednesday, September 26, 12
RIG-I 1.30 uninfected -0.74 Lassa Wednesday, September 26, 12
RIG-I 2.83 1.30 3 dpi 1.10 uninfected -0.74 Lassa Wednesday, September 26, 12
RIG-I 2.83 4.72 1.30 3 dpi 3 dpi 3.24 4.30 1.10 uninfected uninfected -0.74 2.37 Lassa Marburg Wednesday, September 26, 12
Wednesday, September 26, 12
uninfected-2 dpi 3 dpi-12 dpi Wednesday, September 26, 12
uninfected-2 dpi 3 dpi-12 dpi Lassa Marburg Wednesday, September 26, 12
uninfected-2 dpi 3 dpi-12 dpi Lassa Marburg TP FP 34 0 FN TN 0 38 Wednesday, September 26, 12
uninfected-2 dpi 3 dpi-12 dpi Lassa Marburg TP FP 34 0 FN TN 0 38 Wednesday, September 26, 12
uninfected-2 dpi 3 dpi-12 dpi Sensitivity: 1 Specificity: 1 Lassa Marburg TP FP 34 0 FN TN 0 38 Wednesday, September 26, 12
uninfected-2 dpi 3 dpi-12 dpi Sensitivity: 0.5 Specificity: 1 Lassa Blind Marburg TP FP Lassa Marburg Lassa Marburg 34 0 FN TN 33 53 Wednesday, September 26, 12
uninfected-2 dpi 3 dpi-12 dpi Sensitivity: 0.86 Specificity: 0.88 Marburg Blind Lassa TP FP Blind Marburg Lassa Marburg 38 4 Lassa Marburg FN TN 6 29 Wednesday, September 26, 12
Next Steps Wednesday, September 26, 12
Next Steps Use Agilent v2 microarrays to distinguish between Lassa and Marburg Wednesday, September 26, 12
Next Steps Use Agilent v2 microarrays to distinguish between Lassa and Marburg Use RNA-Seq to identify non-coding RNAs and obtain better resolution of transcriptome Wednesday, September 26, 12

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Lab meeting 25/9

  • 1. Detecting Viral Infections Using Microarrays Nacho Caballero Connor Lab Wednesday, September 26, 12
  • 3. RIG-I uninfected Lassa Wednesday, September 26, 12
  • 4. RIG-I 1.30 uninfected -0.74 Lassa Wednesday, September 26, 12
  • 5. RIG-I 2.83 1.30 3 dpi 1.10 uninfected -0.74 Lassa Wednesday, September 26, 12
  • 6. RIG-I 2.83 4.72 1.30 3 dpi 3 dpi 3.24 4.30 1.10 uninfected uninfected -0.74 2.37 Lassa Marburg Wednesday, September 26, 12
  • 8. uninfected-2 dpi 3 dpi-12 dpi Wednesday, September 26, 12
  • 9. uninfected-2 dpi 3 dpi-12 dpi Lassa Marburg Wednesday, September 26, 12
  • 10. uninfected-2 dpi 3 dpi-12 dpi Lassa Marburg TP FP 34 0 FN TN 0 38 Wednesday, September 26, 12
  • 11. uninfected-2 dpi 3 dpi-12 dpi Lassa Marburg TP FP 34 0 FN TN 0 38 Wednesday, September 26, 12
  • 12. uninfected-2 dpi 3 dpi-12 dpi Sensitivity: 1 Specificity: 1 Lassa Marburg TP FP 34 0 FN TN 0 38 Wednesday, September 26, 12
  • 13. uninfected-2 dpi 3 dpi-12 dpi Sensitivity: 0.5 Specificity: 1 Lassa Blind Marburg TP FP Lassa Marburg Lassa Marburg 34 0 FN TN 33 53 Wednesday, September 26, 12
  • 14. uninfected-2 dpi 3 dpi-12 dpi Sensitivity: 0.86 Specificity: 0.88 Marburg Blind Lassa TP FP Blind Marburg Lassa Marburg 38 4 Lassa Marburg FN TN 6 29 Wednesday, September 26, 12
  • 16. Next Steps Use Agilent v2 microarrays to distinguish between Lassa and Marburg Wednesday, September 26, 12
  • 17. Next Steps Use Agilent v2 microarrays to distinguish between Lassa and Marburg Use RNA-Seq to identify non-coding RNAs and obtain better resolution of transcriptome Wednesday, September 26, 12