User:Alexander S Mikheyev/Notebook/rotifer alien genes/2010/03/31

From OpenWetWare

Jump to: navigation, search
Alien genes Main project page
Previous entry      Next entry


Testing fusion primers

  • Testing whether fusion primers for genes that were amplified on the 26th work correctly. Each forward primer has an amplicon A adapter, a barcode and the rotifer primer. Each reverse primer has a B adapter and a rotifer primer.

PCR conditions

Reaction mixture conc. 1x 7
TopTaq buffer10x17
dNTP mix10 mM each0.21.4
Primer mix5 uM each1
TopTaq (QIAGEN)5U/ul0.050.35
template20 ng/ul0.50.5
  • 95C 3 min (60C 1 min, 95C 5s)x35
  • the histone gene, which is about 600 to 800 bp was amplified with a 50:50 mixture of forward and reverse fusion primers (i.e., so that it can be sequenced from both ends).



  • maybe it makes sense to increase annealing temperature to 35C after a few cycles?

SNARF-1 and RED Rotifer Staining

- A. vaga - ~10-20 rotifers per treament


Test 200ul of 1) 1:1000 dye dilution 2) 1:1200 dye dilution 3) 1:1400 dye dilution all treated with dye for 1 hour

Stock tubes at 50ug - diluted with 9ul of DMSO then diluted to 1:800 with MiliQ pure water

(1) Transfer 3 ml of spring water (pH 4.5-5) to a glass vessel (small glass petri dish or culture tube).

(2) Add 200 µl of 10 mM dye stock. Mix thoroughly. (To make 10 dye stock, resuspend an aliquot containing 50 µg CFDA-SE in 9 µl ultrapure DMSO. Store frozen at –20oC.)) - saved used dye for restaining.

(3) Add healthy, well fed animals to be stained in 40ul total volume (a 1:800 final dilution of dye; 25 µM final concentration)

(4) Incubate at room temperature for 1 hour in a dark location.

(5) Pipette off media in the staining dish and add 200ul autoclaved spring water. Repeat rinse 3-5 times. Rinsing in the dish with retain most of the adults while eggs and juveniles which do not attach as well may be lost. To retain younger animals or if staining in a glass tube: transfer stained animals to a centrifuge tube; spin to pellet all animals; discard supernatant, taking care to not disrupt the animal pellet; add autoclaved spring water. Repeat 3-5 times.

(6) Incubate the stained animals for 15 minutes at room temperature in 200ul filtered spring water.

(7) Visualize in the GFP channel of a fluorescent microscope.


Snarf-1 1) 1:1000 dye dilution - alive stained 2) 1:1200 dye dilution - alive stained 3) 1:1400 dye dilution - alive stained

Red 1) 1:1000 dye dilution - weak stain 2) 1:1200 dye dilution - weak stain 3) 1:1400 dye dilution - weak stain

8 days later

Snarf-1 - Rotifers still alive and stained, but lots of background. Probably due to stained food being consumed and waste accumulation. 1:1000 best

Testing of extracted genome

Reaction mixture conc. 1x x16.5 ' lane '
Temp??227Ithaca 2 A3
TopTaq Buffer10x116.528Ithaca 2 A4
dNTP mix10 mM each0.23.329Ithaca 2 A5
Primer mix (HIS F/R1)5 uM each116.537Tsukuba 3 D2
TopTaq5 U/ul0.050.82540Woods Hole 1 A6
Milli Q5.7594.87543Yokohama B5
10 ul47Harvard A1
48Ithaca 2 A6
PCR cycle49Pennsylvania (PA) D4
94C3 min50Tsukuba 1 B5
51Yokohama A2
98C10 sec55Yokohama B2
60C3 minAVAdineta vaga
72C5 min


Personal tools