Matt:LabNotes/2015-6-23: Difference between revisions

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>Mzcai
(Created page with "=Test Mouse Embryo Pre-Processing Protocol for DARTFISH= *For project using DARTFISH on mouse embryo to study cell lineage in cardiac development *They normally fix, permeabil...")
 
>Mzcai
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===Procedure===
===Procedure===
#Make PBT: 1X PBS + 0.1% Triton-X
#Make PBT: 1X PBS + 0.1% Triton-X
#Rehydrate embryo #3
#Rehydrate embryo #3 and #4 in 200ul PCR tube with attached caps
#*75% MeOH in PBT for 10min rotating
#*75% MeOH in PBT for 10min rotating
#*50% MeOH in PBT for 10min rotating
#*50% MeOH in PBT for 10min rotating
#*25% MeOH in PBT for 10min rotating
#*25% MeOH in PBT for 10min rotating
#*PBT for 10min rotating twice
#*PBT for 10min rotating twice
 
#Only for embryo #4
*At this point go into 0.25% Triton-X and 0.01% Pepsin?
#*Add 0.25% Triton-X in 1X PBS for 10min
*Or do ISH protocol and do 6% hydrogen peroxide, ProK, and fix again...
#*Add 0.01% Pepsin in 0.1N HCl for 5min
#Wash with 1X PBS three times
#Make RT Mix (2X volume) '''on ice'''
#*H2O - 314ul
#*M-MuLV RT Buffer 10X - 40ul
#*dNTP 25mM- 4ul
#*aa-dUTP 2mM- 8ul
#*FISSEQ_RT primer (nonamer) 100uM - 10ul
#*RNase Inhibitor 40U/ul- 4ul
#*M-MuLV RTase 100U/ul- 20ul
#Add 200ul RT Mix to embryos and incubate for 10min at 4C and then incubate overnight at 37C

Revision as of 21:45, 25 June 2015

Test Mouse Embryo Pre-Processing Protocol for DARTFISH

  • For project using DARTFISH on mouse embryo to study cell lineage in cardiac development
  • They normally fix, permeabilize, and hybridize probes all in tube suspension (whole mount ISH)
    • They use 20X objective to image the whole 250um depth
      • Since we used 63X objective with 1.4 NA we probably cannot do 250um depth and will require sectioning

ISH Protocol

  • Protocol.pdf
    • Fixed, dehydrated in methanol, and stored in -20C
    • Rehydrated and permeabilized with ProK for ISH

Fixed samples

FISSEQ

  • To save padlock probes will test fixation/permeabilization sample conditions with FISSEQ
  • Will use universal probe for all rolonies (FISSEQ_Adpt Cy3?) to check
  • To image, sandwich embryo between glass slide and coverslip

Procedure

  1. Make PBT: 1X PBS + 0.1% Triton-X
  2. Rehydrate embryo #3 and #4 in 200ul PCR tube with attached caps
    • 75% MeOH in PBT for 10min rotating
    • 50% MeOH in PBT for 10min rotating
    • 25% MeOH in PBT for 10min rotating
    • PBT for 10min rotating twice
  3. Only for embryo #4
    • Add 0.25% Triton-X in 1X PBS for 10min
    • Add 0.01% Pepsin in 0.1N HCl for 5min
  4. Wash with 1X PBS three times
  5. Make RT Mix (2X volume) on ice
    • H2O - 314ul
    • M-MuLV RT Buffer 10X - 40ul
    • dNTP 25mM- 4ul
    • aa-dUTP 2mM- 8ul
    • FISSEQ_RT primer (nonamer) 100uM - 10ul
    • RNase Inhibitor 40U/ul- 4ul
    • M-MuLV RTase 100U/ul- 20ul
  6. Add 200ul RT Mix to embryos and incubate for 10min at 4C and then incubate overnight at 37C