Matt:LabNotes/2017-6-7: Difference between revisions

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   Program
   Program
   98C 1min -> (98C 10s -> 52C 20s -> 72C 20s)x26 -> 72C 3min
   98C 1min -> (98C 10s -> 52C 20s -> 72C 20s)x26 -> 72C 3min
<!--
 
===Results===
===Results===
[[Media:20170523_qPCR_PPcapture_SplintRformamide.xlsx|raw data here]]<br>
[[Media:20170610_qPCR_PPcapture_SplintRformamide.xlsx|raw data here]]<br>
[[File:20170523_qPCR_PPcapture_SplintRformamide_ScatterPlot.PNG|450px]]
[[File:20170610_qPCR_PPcapture_SplintRformamide_ScatterPlot.PNG|450px]]
 
==Repeat qPCR with 1/100 dilution==
*For all 16 samples
*Do 2 serial dilutions of 1/10 to get 1/100
**3ul + 27ul H2O -> 3ul + 27ul H2O
 
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Components'''
| align="center" style="background:#f0f0f0;"|'''1X Volume'''
| align="center" style="background:#f0f0f0;"|'''48X Volume'''
|-
| Captured template diluted 1:100||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
==Conclusion==
  98C 1min -> (98C 10s -> 52C 20s -> 72C 20s)x26 -> 72C 3min
*Finally got a linear trend that makes sense for increasing formamide
-->
*5% formamide or 10% DMF is best

Latest revision as of 22:42, 12 June 2017

Sixth Try: in tube SplintR Test with formamide[edit]

  • Repeat Fifth Try with 95C 3min denature before hybridization

Test Conditions[edit]

  1. Standard: SplintR only
  2. SplintR + 5% formamide
  3. SplintR + 10% formamide
  4. SplintR + 15% formamide
  5. SplintR + 1M Betaine
  6. SplintR + 10% dimethylformamide
  7. SplintR + 5% DMSO
  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 DMF Betaine DMSO H2O Total
1 SplintR 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 0 0 0 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 0 0 0 21 or 20.1 30
3 SplintR + 10% formamide 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 3 0 0 0 19.5 or 18.6 30
4 SplintR + 15% formamide 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 4.5 0 0 0 18 or 17.1 30
5 SplintR + 10% DMF 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 0 3 0 0 19.5 or 18.6 30
6 SplintR + 1M Betaine 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 0 0 6 0 16.5 or 15.6 30
7 SplintR + 5% DMSO 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 0 0 0 1.5 21 or 20.1 30
8 Ampligase 4.5 or 5.4 (0.9ul of each 1uM oligo) 3 0 0 0 0 22.5 or 21.6 30
  1. Combine padlock probes and template in 1X Ligase buffer and possibly additives
  2. Add mineral oil on top
  3. Incubate at 95C for 3min
  4. Incubate at 55C for 18hr
  5. To sample 8 add 3ul Ampligase Mix and incubate at 55C for 1hr30min
    • Ampligase Mix: 1ul Ampligase + 1ul 10X Ampligase Buffer + 8ul H2O
  6. Move samples 1-7 to 37C
    • Move one tube at a time and add enzyme after holding tube between fingers for 5 sec
  7. Add 3ul SplintR Mix and incubate 15min
    • SplintR Mix: 27ul SplintR + 4.5ul 10X SplintR Buffer + 13.5ul H2O
  8. Incubate at 94C for 5min
  9. Put all samples on ice and add 2ul Exo I/III mix
  10. Incubate at 37C for 1hr
  11. Incubate at 94C for 5min
  12. Purify 20ul with Zymo ssDNA purification kit, elute 20ul
  13. Dilute 5ul in 45ul H2O (10x dilution)
  14. 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]

raw data here
File:20170610 qPCR PPcapture SplintRformamide ScatterPlot.PNG

Conclusion[edit]

  • Finally got a linear trend that makes sense for increasing formamide
  • 5% formamide or 10% DMF is best