Friday 01/31/14

10:50a – 11:50p

Goals Today

  • 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
  • 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

Ph Project


  • 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).

Data anlysis

  • configured new RAID drive (12 TB available).
  • transferred double stain data from PhWt and PhM to new drive.

Chromatin project

Cell staining

  • 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).
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