Hosuk:LabNotes/2013-9-12: Difference between revisions

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====Detail procedure====
====Procedure====
*Prepare two barcoded padlock probes - ACTB, RAB7A
*Prepare two barcoded padlock probes - ACTB, RAB7A


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=====2nd RCA probe=====
=====2nd RCA probe=====
*'''FISSEQ_ppRCA''' : GATATCGGGAAGCTGA*A*G --> 18bp
*'''FISSEQ_ppRCA''' : GATATCGGGAAGCTGA*A*G --> 18bp
====Overall Process====
#Prepare each probes – the concentration of each probes are resuspended to 200uM for each ACTB, RAB7A and 2nd RCA primer.
#Hybridize Padlock probe – mixture: 1uL ACTB + 1uL RAB7A + 98uL 2x SSC
#Add mix, and incubate dish in the oven at 55C for 1hr.
#Prepare Ampligase mix - 1uL AmpLigase + 10uL Buffer + 89uL H2O
#Aspirate PBS in rolony sample and wash with PBS once
#Add AmpLigase mix to sample dish, and incubate in the oven at 45C for 4hr.
#Run 2nd RCA from Padlock probes
*# Pre-anneal RCA primer (2uL of 100uM in 98uL 2x SSC)  60°C for 15min
*# Add RCA master mix with aa-dUTP, run RCA for 20 hr.
# Fix 2nd RCA with BS(PEG)9, and deactivate BS(PEG)9 with Tris pH8.0 treatment
# Check image with Cy3 (for the ACTB or RAB7A gene on 2nd rolonies) and  Cy5 channel (1st rolonies)




*Start at 09/10
*Start at 09/10

Revision as of 18:03, 12 September 2013

Gene decoding with Barcoded Padlock probes

Experimental plan

  • Hybridizing padlock probes on 1st rolonies, and
  • Generate 2nd rolonies over 1st rolonies, and
  • Observe each different fluorescent signal from 2nd rolonies


Procedure

  • Prepare two barcoded padlock probes - ACTB, RAB7A
Padlock probe for ACTB
  • ppACTB : /5Phos/CTGTGCTCGCGGGGCG CTTCAGCTTCCCGATATC CGACGG ACGTATCGGTAGTCGCAACGCA GGCAAAGGCGAGGCT --> 77bp
    • two arms : CTGTGCTCGCGGGGCG, GGCAAAGGCGAGGCT
    • site for decoding probes (dcProbe0-Cy3) : ACGTATCGGTAGTCGCAACGCA --> 22bp
    • site for 2nd RCA probes : CTTCAGCTTCCCGATATC --> 18bp
Padlock probe for RAB7A
  • ppRAB7A : /5Phos/GAAGCGAGAAGGTCCAAGTTCTG CTTCAGCTTCCCGATATC CGACGG GTCTTGCGTGCGATACGGAGTA GAGGAGACTAAACGGAGGACA --> 90bp
    • two arms : GAAGCGAGAAGGTCCAAGTTCTG, GAGGAGACTAAACGGAGGACA
    • site for decoding probes (dcProbe1-Cy3) : GTCTTGCGTGCGATACGGAGTA --> 22bp
    • site for 2nd RCA probes : CTTCAGCTTCCCGATATC --> 18bp
2nd RCA probe
  • FISSEQ_ppRCA : GATATCGGGAAGCTGA*A*G --> 18bp


Overall Process

  1. Prepare each probes – the concentration of each probes are resuspended to 200uM for each ACTB, RAB7A and 2nd RCA primer.
  2. Hybridize Padlock probe – mixture: 1uL ACTB + 1uL RAB7A + 98uL 2x SSC
  3. Add mix, and incubate dish in the oven at 55C for 1hr.
  4. Prepare Ampligase mix - 1uL AmpLigase + 10uL Buffer + 89uL H2O
  5. Aspirate PBS in rolony sample and wash with PBS once
  6. Add AmpLigase mix to sample dish, and incubate in the oven at 45C for 4hr.
  7. Run 2nd RCA from Padlock probes
    1. Pre-anneal RCA primer (2uL of 100uM in 98uL 2x SSC) 60°C for 15min
    2. Add RCA master mix with aa-dUTP, run RCA for 20 hr.
  1. Fix 2nd RCA with BS(PEG)9, and deactivate BS(PEG)9 with Tris pH8.0 treatment
  2. Check image with Cy3 (for the ACTB or RAB7A gene on 2nd rolonies) and Cy5 channel (1st rolonies)



  • Start at 09/10