10:00a – 11:45p
Goals
- Write to Alvaro — try tomorrow
- Reply to Zenklusen — try tomorrow
- Check MiSeq Results in process
- repeat RT reaction with more enzyme — try tomorrow
Project 2
- see notes
- Review writeup
- Install phase ring and phase objective on STORM4, take phase images of cells with artificial drift
Literature
- Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription
- ‘Our results implicate transcription factors as primary mediators of sequence-specific regulation
of gene expression programs, with histone modifications frequently reflecting the primary
regulatory event’ — Really? Not much of a conclusion for a potentionally very interesting dataset. - Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression
- “Our findings imply a fundamental trade-off: although the cell can exploit different promoter classes to
differentially control gene expression using TF dynamics, gene expression noise fundamentally
limits how much information can be encoded in the dynamics of a single TF and reliably decoded by
promoters.” — That doesn’t sound like a trade-off to me. It sounds like a statement of limitation. And like the conclusion of the previous paper, there was already no question that this was true: noise limits information transmission. Despite the un-inspiring opening, the rest of the paper looks interesting.
Probe Making lessons from last round
- 31 round PCRs from short stuff with extra large product not good.
- Deep sequencing — aligning results to fasta file of probes using Jeff’s Matlab scripts and bowtie2
Banff Workshop
- Working on references
- reviewing edits to write-up.
STORM
- Mounted sample D12 DNA upside down, all cells lost.
Cell Culture
- Cells really not adhering. Earlier frozen stock was doing better
- Try taking cells from all remaining frozen stocks and pooling these.
Ph project
- got cells from Ajaz