Matt:LabNotes/2016-5-16

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Test 25um Gel[edit]

Experiment Plan[edit]

  • Goal: Test whether the longer (150bp) padlock probes can diffuse through ~25-50um polyacrylamide hydrogel to generate rolonies
    • Previously worked with ~140um gel

Protocol[edit]

Day 1[edit]

  1. Prepare hydrogel mix
    1. 5% PA Gel: Standard hydrogel
  2. Attach ~25um thick adhesive to Vectabond + Bind-silane treated coverslip
  3. Add 2ul PKP2 beads diluted in 50ul H2O to coverslips right on top of 2 magnets
    • Pipette away extra H2O leaving only dried beads
  4. Inject ~50ul of 200ul hydrogel mix into each dish (underneath another coverslip)
  5. Vacuum seal bag and then pump with Argon gas
  6. Let set at RT for 30min
  7. Attach to bottom of culture dish

Day 2[edit]

  1. Wash with nf-H2O twice
  2. Prepare Ampligase mix on ice
    • Preheat H2O + Padlock probes to 85C and then snap cool before adding Ampligase buffer and enzyme
Component Volume
DEPC-H2O 37
Ampligase Buffer 10
Batch 14 237nM 43
Ampligase 10
Total 100
  1. Add mix to sample and incubate for 30min at 37C
  2. Move sample to 60C and oven slowly decreases to 55C and held for ~24hr

Day 3[edit]

  1. Wash with 1X PBS once
  2. Add 1uM FISSEQ_ppRCA (1ul 200uM FISSEQ_ppRCA + 199ul 2X SSC + 30% formamide) and incubate 1hr at 55C
    • Preheated to 70C before adding
  3. Wash with 2X SSC once, 1X SSC once, and 1X PBS once
  4. Add RCA mix and incubate 15hr at 30C
Component Volume
H2O 174
10X Phi29 Buffer 20
25mM dNTP 2
4mM aa-dUTP 2
Phi 29 (low conc) 2
Total 200

Day 4[edit]

  1. Wash with 1X PBS once
  2. Add 200ul BS(PEG)9 (4ul BS(PEG)9 + 196ul 1X PBS) for 1hr at RT
  3. Wash with 1X PBS twice
  4. Add 1M Tris ph8.0 for 30min at RT
  5. Wash with 1X PBS twice and store in 2ml 1X PBS

Imaging[edit]

  • 8-bit to save space
  • 20X Objective for larger field of view


Hybridize FISGA_Adpt Cy3[edit]

  1. Preheat 200ul 0.5uM FISGA_Adpt_Cy3 in 30% formamide 2X SSC to 75C
  2. Add 200ul to each dish and let sit for 10min at RT
  3. Wash twice with 2X SSC

File:MAX Beads FISGAadpt Cy3.jpg

Strip[edit]

  1. Preheat 80% formamide 2X SSC to 75C
  2. Add 200ul to Dish1 (PosCtrl) and let sit for 15min at RT
  3. Wash twice with 1X PBS
  4. Add 500ul 1X PBS to image

File:MAX Beads 15min 2xWash.jpg

Conclusion[edit]

  • 25-50um (Kapton tape thickness) 5% PA Gel is thin enough that a single round of stripping/washing completely removes signal