9:00 am – 8:00 pm
Ph project
Figure making
- revising layout of Fig 5
- sent to team
- NF says a bit too tight, need more whitespace.
- re-arranged panels again
MERFISH
- exploring probe selection criteria
- compare variable length probes to 20mers with 20% GC range (35-55%)
Building better transcriptome
- approach: combining ENCODE data from multiple cell lines to get a broader swath of genes that are appreciably on.
- selected cell lines: ‘a549′,’daoy’,’hct116′,’imr90′,’mcf7′,’panc1′,’t47d’,’u2os’
- require gene to be at FPKM > 1E-5 in one of these cell lines.
- challenge 1: need to chose an isoform to build probes to
- challenge: isoforms rather cell specific:
- current solution: select isoform with the highest average expression across all cell lines.
- new human transcriptome representing expression FPKM >10^-5 now running
- note 20K of these 45K genes has FPKM > 1 in one of these cell lines.