Monday 05/27/13

11:00 A – 10:00 P

Probe and hybe troubleshooting

• check staining
• AATAT control and Y look good
• black maybe stained, check after washout
• low and high RNA-en-P1 both have substantial nuclear background, but no clear signal

Coding

• Fixed bugs in CalcChromeWarp from migration to few globals and multi-instance support.
• Also fixed bug resulting from two molecules mapping the same reference bead.
• finished calculating warp map for ph-wt 488 vs 647 flag data.
• large clusters have good correspondence but small clusters don’t.
• see post

To test

• My embryo RNA FISH probes (neur, alpha-Tub, Tkv) on cultured cells using ‘3D FISH’ cell prep.
• for tomorrow:
• long secondary + 405 teritary (vs. short secondary)
• test with en and AATAT (?)

PCR

• Small scale
  1. 2x en-T7 P1
  2. 2x en-T7 P1rc
  3. AbdA + P1 adapter
  4. AbdB + P1 adapter
  5. test 1 of Ubx-P1-a + CPPT
  6. test 1 of BXC-P1-a + CPPT
• 2 mL scale PCR
  1. Ubx-adapterP1 + CPPT
  2. AbdA-adapterP1 + CPPT
  3. AbdB-adapterP1 + CPPT
  4. BXC-adapterP1 + CPPT