10:50a – 11:50p
- Order primers for sequencing
- work on Ph manuscript
- finish hybes to test sample age
- image F03F04 samples
Deep sequencing 2
- probes to order with sequencing indices
- D12 (375kb) GTGTCGCGTCGGCCAGAAAC
- F11 (180kb) AGGACATTCGCGGCTTTCAG
- G09 (76kb) CGTCGCGTTGGATTCAAGAG
- F12 (17kb) GCGAACGGGCGAACTGTTAC
- probes from Hao’s library to order with sequencing indices
- Foward primers: add NEB-universal
- reverse primers: add NEB-idnex
- Jeff’s new dual indexing primers
- added to primer table with NEB sequencing adapters
Some interesting literature
- working on figures
- Just stats:
- just clusters (no weighting)
- Ph-Flag: 552,497 unique clusters from 17 cells
- PhM-Flag: 872,640 unique clusters from 34 cells
- S2 wt cntrl: 474,832, unique clusters from 42 cells
- KS test of PhWT-flag to S2 1.2E-64.
- KS test of S2 to WT is 0.
- sent revised Fig 1 to Ajaz (has group meeting again. Kingston lab seems to have group meetings quite a lot more frequently).
- configured new RAID drive (12 TB available).
- transferred double stain data from PhWt and PhM to new drive.
- finish hybes with fresh cells of F03+F04 G01+G02
- STORM of F03+F04. Calbiration spots very bright large conventional, still much tighter than last time. Further evidence that we had a cell degradation issue
- I think this partially also affected the ANTC that were imaged a week before the FO3+F04 last time. Let’s repeat that too.
- New stains: ANTC (1.1 uL of primary each, .5 uL of secondary). Also G05 alone, and G09 repeat (though I’m pretty sure this one was fine. Can always use repeats, and I actually made a very good batch of this probe).