8:50a – 5:10p, 8:30p – 10:40p
Other stuff
- write to landlady about move in
- return keys for 2nd floor
Coding
- fixed bug in
STORMfinderBeta.m - For Hao for updates: Fork fast-forward https://github.com/blog/266-fast-forward-your-fork
Data Analysis
- copying files to ProRAID while running splitQVdax is very slow both ways (G3 and G6 data)
- Much, much faster to run one copy of splitQVdax on ProRAID and other copy on STORM2 Temp drive (and copy that later).
- Running STORM analysis on G3 and G6 data.
samples priority:
- Yellow: E6, E7, E10, F6,
yellow
- 5kb Y: G07 alphaTub
- 10kb Y: F02 BXY_Y left 15 kb
- 10kb Y: F12 Taf1 Y/G
- 10kb Y: E06 EPc, 12 kb
- 10kb Y: E07 Tou 15 kb
- 50kb Y: G06 AlphaTub region
- 100kb Y: E10 98 kb pure yellow
- 100kb Y: F06 BXC_right 140kb Y/R
- 400kb Y: D12 385kb Y region. (well never got loaded)
black
- 10 kb black domain: D09, next to Red3
- 10 kb black domain: F09, next to RED1
- 50 kb black domain: G08, between GRN and ANTC
- 50 kb black domain: E05, upstream of E(Pc)
- 100 kb black domain: F01, BXC_K_left, 125kb,
- 250 kb black domain: F07, BXC_K_right, 240kb,
- 250 kb black domain: F11 ANTC-L 180kb
- 500 kb black domain: F10, 478kb region, on 3R.
- 500 kb black domain: G10, 425 kb on X
Green
- 200 kb green domain: E01: has isolated boundaries. only 321 probes
Probe Making
RNA cleanup
- samples E6, E7, E10, F6
- wide range of RNA concentrations (100 – 800 ng/uL RNA in 100uL).
- RT reactions (40uL)
- buffer = 8uL buffer + 4uL DTT + 2 uL RNasin + 1 uL enzyme.
- 2 uL 100mM primer (200 pmol) + 2uL dNTPs + 21 uL RNA. (4 uL primer for F6)
- doing 405-primer and P1-common primer reactions for each sample.
- Moved Plate of RNA templates from T7 reaction to -80C (new box behind my current box).
- completed Oligo-cleanup. E6 very high yield. E7 and E10 probably failed, concentration is essentially that of primer.
Cell culture
- new media and passaged 75cm flask of Kc167 cells
- stopped Clone8 culture