Tuesday, 08/06/13

9:45 A – 7:00 P, 8:30 P – 12:15 A

Meeting prep STORM analysis

• analyzing temperature data
• about 75% fewer localizations at 52C than 47C
• little change in background / off-target localizations
  
• Running automated analysis of color data
• Automated analysis of background doesn’t do good job separating cells. Results easier to interpret as total localization per spot vs total localizations in cell.
• Manually segment cells for a bunch of randomly selected images in each data set, compute ratio.
• Record and plot results.

Discussion

• plans for testing new probe design. JM will test RT plate format next week
• Hao and I will test RNA
• CMOS demo on STORM probably start next week.
• not sure at present how much rebuilding will be necessary to mount the camera, but will try to be reversible
• STORM4 might be available but Yari and Colenso are both back from travel and planning experiments on small scale (~36hr).
• STORM4 750 laser is still subpar – 50 mW at the fiber.

Analysis

• Trying to understand differences in BX-C structure between Clone8 and S2/Kc167 cells
• full name of clone8 = CME W1 Cl.8+
• UCSC genome browser data upload doesn’t work if file extension does not match file type. Wig formatted transcription profiling data from modEncode has a .gr extension after unpacking, not a .wig, and won’t load.
• also need to ensure chromosome names have “chr” in front (not just 2L, chr2L).
• comparing RNA expression profiling results in clone8 vs S2R+, Kc167 and S3.
• all look pretty similar. But rather different absolute scales on y-axis
  

Peak expression in zone:

Mean expression (arbitrary units)