Daniel:Notebook/RNAFISH/2015-2-5: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Djacobse
(Created page with "=Cell Line FISH= Back to Calendar ==Slide Preparation== #Prepare a cell suspension of 500 000-2 000 000 cells/mL in culture media #Add 20 uL of ...")
 
>Djacobse
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
=Cell Line FISH=
=Cell Line RNA FISH=


[[Daniel:Notebook/RNAFISH|Back to Calendar]]
[[Daniel:Notebook/RNAFISH|Back to Calendar]]
Line 9: Line 9:
#Allow cells to adhere for 6 hours at 37 C
#Allow cells to adhere for 6 hours at 37 C
#Rinse slides briefly in 1X PBS
#Rinse slides briefly in 1X PBS
#Fix slides for 5-15 minutes in 4% (v/v) paraformaldehyde in 1X PBS
#Fix slides for 5 minutes in 4% (v/v) paraformaldehyde in 1X PBS
#Rinse briefly in 1X PBS
#Wash 2x in 2xSSPE for 5 minutes each
#Incubate for 5 minutes in 1 mL of 2X SSCT
#Incubate for 5 minutes in 1 mL of 2X SSCT + 50% (v/v) formamide
#Remove media and add 1 mL of 2X SSCT + 50% (v/v) formamide


==Hybridization==
==Hybridization==
'''Sample Matrix'''
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="background-color:#CCC0DA;font-size:12pt;font-weight:bold"
| width="65" height="45"  valign="bottom" | Sample
| width="65" align="center" | uL FOXP2-488
| width="65" align="center" | uL GAD1-594
| width="87" align="center" | uL hybridization buffer
| width="65" align="center" | uL formamide
| width="65" align="center" | uL Total
|- style="font-size:12pt"
|style="font-weight:bold" height="15"  valign="bottom" | A
| align="center" align="center" valign="bottom" | 1
| align="center" align="center" valign="bottom" | 1
| align="center" align="center" valign="bottom" | 20.5
| align="center" align="center" valign="bottom" | 2.5
| align="center" align="center" | 25
|- style="background-color:#D9D9D9;font-size:12pt"
|style="font-weight:bold" height="15"  valign="bottom" | B
| align="center" align="center" valign="bottom" | 2
| align="center" align="center" valign="bottom" | 2
| align="center" align="center" valign="bottom" | 18.5
| align="center" align="center" valign="bottom" | 2.5
| align="center" align="center" | 25
|}


#Permeabilize by leaving at room temperature for 30 minutes in 0.6% Triton X-100/2xSSPEdepc
#Permeabilize by leaving at room temperature for 30 minutes in 0.6% Triton X-100/2xSSPEdepc

Latest revision as of 23:45, 5 February 2015

Cell Line RNA FISH[edit]

Back to Calendar

Slide Preparation[edit]

  1. Prepare a cell suspension of 500 000-2 000 000 cells/mL in culture media
  2. Add 20 uL of cell suspension per dish to the cener; add 80 uL culture media
  3. Allow cells to adhere for 6 hours at 37 C
  4. Rinse slides briefly in 1X PBS
  5. Fix slides for 5 minutes in 4% (v/v) paraformaldehyde in 1X PBS
  6. Wash 2x in 2xSSPE for 5 minutes each

Hybridization[edit]

Sample Matrix

Sample uL FOXP2-488 uL GAD1-594 uL hybridization buffer uL formamide uL Total
A 1 1 20.5 2.5 25
B 2 2 18.5 2.5 25
  1. Permeabilize by leaving at room temperature for 30 minutes in 0.6% Triton X-100/2xSSPEdepc
  2. Wash 2x for 5 minutes in 2X SSPE
  3. Dehydrate in 30, 50, 70, 100, 100 ethanols 2 mins ea.
    1. Make solutions from absolute ethanol and depc/H20*.
  4. Dry in oven at 50-65C.
  5. Prehybridize slides ~ 1 hour+ at 70C with prehybridization solution
  6. Determine probe concentration (usually 2-4ng/ul) and denature probe at 90C for 10-15 minutes.
  7. Drop temp to 65C
  8. Spin briefly. Do not open the tube when it is at 90C-probe loss can occur.
  9. Add about 50-100 ng of probe to each slide in appropriate buffer; should be ~25 uL
  10. Seal coverslip with rubber cement, wait ~5 minutes for cement to dry
  11. Hybridize overnight appropriate 37C
  • Prehybridization solution:
    • 50% deionized formamide
    • 50% 2xSSC pH 7.0
    • Add dextran sulfate to 1%
  • Hybridization solution (Arjun Raj)
    • 2X SSC
    • 10% Formamide
    • 10% Dextran Sulfate
    • 0.02% RNAse-free BSA
    • 50 μg E.coli tRNA