Tuesday 06/30/15

9:45 am – 7:30 pm, 8:30 pm – 10:00 pm

RNAi

• setup RNase digestions
• fixed cells (probably too late for these guys, actually started Tuesday night).

Primer design

• would be useful to do by batch in matlab rather than manually
• looking up existing matlab functions for getting gene sequences etc.
• troubleshooting
  • getgenbank returns over a quarter million features when called on Drosophila abd-B. (32 Mb of sequences mapping to unassembled parts of the chromosome). actually it’s all of Chr3R, starting from heterochromatic bases
  • need to use the nucleotide search option in genbank, search for gene name and melanogaster, select transcript, get accession number of that.
• exploring Jeff’s DesignPrimers wrapper for primer3.
• installed primer3 (best to get the windows binary version)
• Completely awesome (as expected). Could use a Tm choice feature?
• primers designed for
  'Abd-B','NM_001275719';
'abd-A','NM_169733';
'Ubx','NM_169728';
'en','NM_078976';
'Antp','NM_206445';
'Dfd','NM_057853';
'lab','NM_001260024';
'Pc','NM_079475';
'Psc','NM_001299439';
'Esc','NM_058083';
'ph-p','NM_001297873';
'ph-d','AM943679';
'pho','NM_166827';
'Sce','NM_058161';
'Su(z)2','NM_079002';
'Scm','NM_001260077';

Orders

• ordered BG3-cl2 cells
• ordered NEB sequencing kit (to replace elements I’ll use from JM/SW stocks)
• ordered primer plate (all Fwd primers, then all rev primers)

To do

• set up new RNAi experiments
• design primers