Matt:LabNotes/2017-5-15: Difference between revisions

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[[Media:20170517_qPCR_PPcapture_SplintRformamide.xlsx|analysis here]]<br>
[[Media:20170517_qPCR_PPcapture_SplintRformamide.xlsx|analysis here]]<br>
[[File:20170517_qPCR_PPcapture_SplintRformamide_ScatterPlot.PNG|450px]]
[[File:20170517_qPCR_PPcapture_SplintRformamide_ScatterPlot.PNG|450px]]
==Conclusion==
*Confirms 2nd try
*Dr. Zhang suggested doing 95C denature step before 55C hybridization to remove secondary structures in padlock probes
**Padlock probes are ~80bp

Latest revision as of 00:18, 3 June 2017

Third Try: in tube SplintR Test with formamide and ET SSB[edit]

Test Conditions[edit]

  1. Standard: SplintR only
  2. SplintR + 5% formamide
  3. SplintR + 7.5% formamide
  4. SplintR + 10% formamide
  5. SplintR + 12.5% formamide
  6. SplintR + 15% formamide
  7. SplintR + 17.5% formamide
  8. Positive Control: Ampligase
  • For each test conditions have
    • one sample with ALL padlock probes and template
      • Should see amplification
    • one sample with all padlock probes with NO MALAT1 template
      • Should not see amplification

Padlock Probes and Template[edit]

  • ppCUX2
  • ppBCL11B
  • ppRELN_1
  • ppGFAP
  • ppMALAT1
    • /5Phos/TTTCTGCCTTTACTTATCAATTCCTTCAGCTTCCCGATATCCGACGGTCTACTTCGTCGCGTCAGACCAAATGGAGGTATGACATATAATCT
  • Template for ppMALAT1: MALAT1_template
    • /5AmMC6/GAATTGATAAGTAAAGGCAGAAA AGATTATATGTCATACCTCCAT

Protocol[edit]

Sample # Condition 30nM PP + Template 10X Buffer Formamide H2O Total
1 SplintR 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 0 22.5 or 21.6 30
2 SplintR + 5% formamide 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 1.5 21 or 20.1 30
3 SplintR + 7.5% formamide 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 2.25 20.25 or 19.35 30
4 SplintR + 10% formamide 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 3 19.5 or 18.6 30
5 SplintR + 12.5% formamide 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 3.75 18.75 or 17.85 30
6 SplintR + 15% formamide 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 4.5 18 or 17.1 30
7 SplintR + 17.5 formamide 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 5.25 17.25 or 16.35 30
8 Ampligase 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 0 25.2 or 22.5 (these were added before realizing wrong volume. Kept as is) 30
  1. Combine padlock probes and template in 1X Ligase buffer and possibly formamide
  2. Add mineral oil on top
  3. Incubate at 55C for 18hr
  4. To sample 8 add 3ul Ampligase Mix and incubate at 55C for 1hr30min
    • Ampligase Mix: 1ul Ampligase + 1ul 10X Ampligase Buffer + 8ul H2O
  5. Move samples 1-7 to 37C
  6. Add 3ul SplintR Mix and incubate 15min
    • SplintR Mix: 27ul SplintR + 4.5ul 10X SplintR Buffer + 13.5ul H2O
  7. Incubate at 94C for 10min
  8. Put all samples on ice and add 2ul Exo I/III mix
  9. Incubate at 37C for 1hr
  10. Incubate at 94C for 10min
  11. qPCR all 16 samples with triplicates
Components 1X Volume 48X Volume
Captured template 1 0
10uM ISB_CA_AF 0.4 19.2
10uM ISB_CA_AR.T2 0.4 19.2
2X KAPA SYBG MM 12.5 600
H2O 10.7 513.6
Total 25 1,152
  • Aliquot 24ul from 48X master mix and add 1ul captured template
 Program
 98C 1min -> (98C 10s -> 52C 20s -> 72C 20s)x26 -> 72C 3min

Results[edit]

analysis here
File:20170517 qPCR PPcapture SplintRformamide ScatterPlot.PNG

Conclusion[edit]

  • Confirms 2nd try
  • Dr. Zhang suggested doing 95C denature step before 55C hybridization to remove secondary structures in padlock probes
    • Padlock probes are ~80bp