Alistair's Lab Notebook

4:00 pm – 8:00 pm

Ph-polymerization

• working on response to reviewers, round 2
• analyzing cluster density of negative controls
  • see new quantification in project Data folder

Kc cell seq prep

• passage newly plated cells (10/05) into larger flasks (in SFX)
• allow cells to grow and attach overnight.

exploring tSNE (11 am -3:50 pm)

• looking at L7 data
• see the expected correlations (here in 3D)
  
• can also see dataset biases (these go away on z-normalization).
  
  
• 1000 gene data
  
• not so good for chromatin structure yet
  • algorithm cares about absolute orientation (forward and backward slanty 1s are different, 6s and 9s are different).
  • could do some sort of global rotation to fix this, which would rotate all 1s in same direction
  • still wouldn’t capture features likes lots of protrusions — its hierarchical clustering of absolute distances of the measurements.
• obviously our data descriptors like volume still have interesting affects on the data
  
  
  

1:00 pm – 7:00 pm, 8:30 pm – 9:45 pm

job apps

• revising research statement (remotely 9:00 am – 1:00 pm)
• sent to a few colleagues and XZ for comments
• working on teaching statement 5:00 pm – 7:00 pm

QPCR

• BB testing KD
• 70% KD efficiency (down from 80-90)
• options
  • have more of the prepped sample from last time, can run as a technical replicate at higher concentration to address the 0 reads issue.
  • might have more RNA in the freezer (not sure about this)
  • have more cDNA from QPCR experiments. should be able to prep this for sequencing. won’t have the easy length control. Maybe not a big problem for the reads — might have to do some adjustment of PCR amplification step.

9:00 am

job apps

• working on figures for research proposal, 9:00 am

Manuscript

• working on revisions.