Daniel:Notebook/HiResChrPaint/2014-7-19: Difference between revisions

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>Djacobse
>Djacobse
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==FISH Hybridization==
==FISH Hybridization==
'''Sample Matrix'''
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="background-color:#8DB4E2;font-size:12pt" align="center"
|style="font-weight:bold" width="65" height="30" | Sample
|style="text-decoration:underline;color:#0000FF" width="65" |  [http://genome-tech.ucsd.edu/LabNotes/index.php/Daniel:Notebook/HiResChrPaint/2014-1-24 Cot1-488 (ug)]
|style="font-weight:bold;text-decoration:none" width="65" | Dystrophin-488 (pmol)
|style="font-weight:bold" width="65" | Dystrophin-546 (pmol)
|style="font-weight:bold" width="65" | Cot1 (ug)
|- style="font-size:12pt" align="center"
|style="font-weight:bold" height="15" | A
| align="center" | 0
| 8.6 (30)
| align="center" | 0
| 2.5 (2.5)
|- style="background-color:#D9D9D9;font-size:12pt" align="center"
|style="font-weight:bold" height="15" | B
| align="center" | 0
| align="center" | 0
| 7.9 (30)
| 2.5 (2.5)
|- style="font-size:12pt" align="center"
|style="font-weight:bold" height="15" | C
| 5 (0.4)
| align="center" | 0
| align="center" | 0
| align="center" | 0
|}


#Allow stored samples to warm to room temperature
#Allow stored samples to warm to room temperature

Revision as of 22:11, 19 July 2014

Dystrophin Probes (Started 7/18/2014)

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Dye Labeling

  1. Warm DMSO and bicarbonate labeling buffer and nuclease free water to room temperature
  2. Add 5 uL DNA and 3 uL of sodium bicarbonate buffer
  3. Denature samples for 5 minutes at 95C, then snap cool using ice box
  4. Dissolve 1 vial of reactive dye in 2 uL solvent; vortex ≥10 seconds
    1. dye cannot be saved for later use. Use immediately!
  5. Add 2 uL dye to sample
  6. Incubate in the dark for 1 hour
  7. Add 5 uL 3M NaOAc and 40 uL nfH20 to sample
  8. Recommend column purification after incubation

Labeling Results

Sample ng/uL ssDNA pmol/uL dye pmol/uL ssDNA dye/probe bp:dye ratio
Dystrophin-488 23.3 3.9 3.5 1.1 18
Dystrophin-546 25.2 5.5 3.8 1.4 14

Good labeling results. Proceeding to FISH.

FISH Hybridization

Sample Matrix

Sample Cot1-488 (ug) Dystrophin-488 (pmol) Dystrophin-546 (pmol) Cot1 (ug)
A 0 8.6 (30) 0 2.5 (2.5)
B 0 0 7.9 (30) 2.5 (2.5)
C 5 (0.4) 0 0 0
  1. Allow stored samples to warm to room temperature
  2. Incubate in 2X SSCT +50% (v/v) formamide for 2.5 minutes at 92 C in pre-warmed media
  3. Incubate in 2X SSCT + 50% formamide at 60C for 20 minutes
  4. Remove samples and allow to cool to room temperature
  5. Add 25 uL hybridization cocktail to center
  6. Add 22x22 #1.5 coverslip; seal with rubber cement
  7. Allow the rubber cement to air-dry for 5 minutes at room temperature
  8. Denature for 2.5 minutes at 92C; keep humid
  9. Transfer slides to a humidified chamber and hybridize overnight at 42C