Matt:LabNotes/2016-11-16: Difference between revisions

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=DARTFISH on ___ with SplintR in PA Gel=
=DARTFISH on 5342 Occipital Cortex with SplintR in PA Gel=
*Try 1 sample with polyacrylamide gel added [[Matt:LabNotes/2016-8-3|after permeabilization]]
*Try 1 sample with polyacrylamide gel added [[Matt:LabNotes/2016-8-3|after permeabilization]]
*Used 100nM padlock probe
*Used 100nM padlock probe
*Sample: GTEx Patient 5342?
*Sample: GTEx Patient 5342 Occipital Cortex


*5% Gel mix and protocol is same as [[Matt:LabNotes/2016-6-28#Gel_Mix|this with Acryloyl-X]]
*5% Gel mix and protocol is same as [[Matt:LabNotes/2016-6-28#Gel_Mix|this with Acryloyl-X]]
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#*2ul 1%Pepsin + 10ul 2N HCl + 188ul H2O
#*2ul 1%Pepsin + 10ul 2N HCl + 188ul H2O
#Wash with nf-1X PBS three times '''and check for degradation'''
#Wash with nf-1X PBS three times '''and check for degradation'''
#*First try ALL the tissue sloughed off by the end of 3rd wash
#Aspirate any liquid and place a glass slide with 50um spacer over the coverslip with tissue
#Aspirate any liquid and place a glass slide with 50um spacer over the coverslip with tissue
#*Secure in plastic jig
#*Secure in plastic jig
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| Total||100
| Total||100
|}
|}
#Move sample to 60C and oven slowly decreases to 55C and held for ~24hr
#Move sample to 60C oven and slowly decreases to 55C and held for ~24hr
 
<!--
===Day 2===
===Day 2===
#Wash with 1X PBS twice preheated to 55C
#Wash with 1X PBS twice preheated to 55C

Revision as of 22:12, 18 November 2016

DARTFISH on 5342 Occipital Cortex with SplintR in PA Gel

  • Try 1 sample with polyacrylamide gel added after permeabilization
  • Used 100nM padlock probe
  • Sample: GTEx Patient 5342 Occipital Cortex
Component Volume
40% AB 199:1 Mix 6.25
10% BSA 1
10mg/ml Acryloyl-X, SE in DMSO 1
H2O 39.75
5% TEMED 1
5% APS 1
Total 50

Protocol

Day 1

  1. Prepare plastic culture dish with 12x17mm hole, tweezers, large plastic dish, and 50C hot plate
    • EtOH and UV sterilize
  2. Made 4% PFA in 1X PBS
    • 10ml 16% PFA + 4ml 10X PBS + 26ml H2O
  3. Take out brain section from -80C and dry on 50C hot plate for 3min
  4. Submerge coverslip in 5ml 4% PFA in petri dish for 15min at 37C
  5. Wash twice with cold 1X SSPE by submerging
  6. Add 0.25% TX-100 in 2XSSPE and incubate 10min at RT
  7. Wash with cold nf-H2O three times and check for degradation
  8. Add 0.01% Pepsin in 0.1N HCl and incubate for 90sec at 37C
    • 2ul 1%Pepsin + 10ul 2N HCl + 188ul H2O
  9. Wash with nf-1X PBS three times and check for degradation
    • First try ALL the tissue sloughed off by the end of 3rd wash
  10. Aspirate any liquid and place a glass slide with 50um spacer over the coverslip with tissue
    • Secure in plastic jig
  11. Add 50ul gel casting mix filtered and degassed
  12. Seal in plastic bag and vacuum out air before filling with argon
  13. Let sit at RT for 30min
  14. Aspirate non-polymerized gel and wash once with 1X PBS
  15. Attach coverslip to bottom of petri dish
  16. Aspirate non-polymerized gel and wash once with 1X PBS
  17. Prepare SplintR Mix
    • Preheat Padlock Probes then snap cool
Component Volume
10X SplintR Buffer 10
CA12kOct2016_V4 160nM 60
H2O 30
Total 100
  1. Move sample to 60C oven and slowly decreases to 55C and held for ~24hr