Matt:LabNotes/2016-6-24: Difference between revisions
Jump to navigation
Jump to search
>Mzcai mNo edit summary |
>Mzcai m (→PAGE Check) |
||
(3 intermediate revisions by the same user not shown) | |||
Line 119: | Line 119: | ||
98C 30s -> (98C 10s -> 52C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x21 | 98C 30s -> (98C 10s -> 52C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x21 | ||
[[450px]] | [[File:2016-06-27_TB12kApr2016_V7_intubecapture_testPCR.jpg|450px]] | ||
====PCR==== | ====PCR==== | ||
{| {{table}} | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''Components''' | | align="center" style="background:#f0f0f0;"|'''Components''' | ||
| align="center" style="background:#f0f0f0;"|'''1X Volume''' | | align="center" style="background:#f0f0f0;"|'''1X Volume''' | ||
| align="center" style="background:#f0f0f0;"|''' | | align="center" style="background:#f0f0f0;"|'''2.5X Volume''' | ||
|- | |- | ||
| Captured template||12||0 | | Captured template||12||0 | ||
|- | |- | ||
| 10uM Forward Primer||2|| | | 10uM Forward Primer||2||5 | ||
|- | |- | ||
| 10uM Reverse Primer||2||0 | | 10uM Reverse Primer||2||0 | ||
|- | |- | ||
| 2X KAPA SYBG MM||50|| | | 2X KAPA SYBG MM||50||125 | ||
|- | |- | ||
| H2O||34|| | | H2O||34||85 | ||
|- | |- | ||
| Total||100|| | | Total||100||250 | ||
|} | |} | ||
Program | Program | ||
98C 30s -> (98C 10s -> 52C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s) | 98C 30s -> (98C 10s -> 52C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x13 -> 72C 3min -> 4C hold | ||
[[File: | [[File:2016-06-27_TB12kApr2016_V7_intubecapture_PCR.jpg|450px]] | ||
*Bead purification with | *Bead purification with 0.8:1 Beads to amplicon volume ratio | ||
**Eluted with 50ul total for each sample | **Eluted with 50ul total for each sample | ||
===PAGE Check=== | ===PAGE Check=== | ||
[[File:2016-06- | [[File:2016-06-28_TB12kApr16V7_CapturegDNA.jpg|250px]] | ||
*Labeled tubes and put in "Non-quantified Sequencing Libraries" | *Labeled tubes and put in "Non-quantified Sequencing Libraries" | ||
** | **Sample: MC20160628_TB12kApr16V7_gDNA-1 (MC160628_TB12kAprV7_gDNA-1) | ||
Latest revision as of 00:51, 29 June 2016
in vitro Capture with TB12k_Apr2016 V7[edit]
- Will capture gDNA from mouse embryonic fibroblasts (got from Andrew)
Sample Groups[edit]
- gDNA MEF (77ng/ul)
- Negative Control
gDNA[edit]
Probe:target | 1000:1 | ' |
Probe size | 1808 | probes |
DNA template | 300 | ng |
gDNA MW | 1.8x10^12 | g/mol |
gDNA (300ng) | 1.66x10^-19 | mol |
Probe (1000:1) | 1.66x10^-16 | mol |
Probe MW (1808, 160nt) | 8.7997168x10^7 | g/mol |
Amount Probe req'd | 14.6 | ng |
- 374nM = 18.2ng/ul
Sample # | Sample Description | Probes | Target | 10X Ampligase Buffer | H2O | Total |
1 | gDNA | 0.8 | 3.9 | 3 | 22.3 | 30 |
2 | NTC | 0.8 | 0 | 3 | 26.2 | 30 |
- Add 40ul Mineral Oil on top
Program
- 95C 30sec -> cool down to 55 C at 0.02C/sec -> 55 C 20h
- In BioRad Thermalcycler program says: -0.2C per cycle every 30sec
- -> add 3ul AmpLigase enzyme mix (0.5U/ul AmpLigase in 1X AmpLigase buffer)
- -> 55 C 20h (actually 24h)-> 94C 2min -> add 2ul Exo I/III mix-> 37C 2h -> 94C 2min -> 4C hold.
- Tiffany accidentally stopped reaction after 30min of Exo I/III digestion
- She let it run 2min at 94C and then put it in fridge
- Soon after, she called and I asked her to add 2ul of fresh Exo I/III and finish out the protocol with 37C 2h -> 94C 2min -> 4C hold
AmpLigase enzyme mix[edit]
Components | Stock conc. | Unit | Final conc. | Unit | Prepare volume 30ul |
AmpLigase | 5 | U/ul | 0.5 | U/ul | 1 |
10x AmpLigase Buffer | 10 | x | 1 | x | 1 |
H2O | 8 | ||||
Total | 10 |
Add Sequence Adapters PCR[edit]
Primers[edit]
Primer | Sequence | Index # |
ISB_CA_AF | AATGATACGGCGACCACCGAGATCTACACGCCTGCATATCGGGAAGCTGAAG | |
ISB_CA_AR.T1 | CAAGCAGAAGACGGCATACGAGATCGTGATCGGTCTGCCTTCCCGATATCCGACGG | Indx1 |
ISB_CA_AR.T2 | CAAGCAGAAGACGGCATACGAGATACATCGCGGTCTGCCTTCCCGATATCCGACGG | Indx2 |
Sample | Index | Forward Primer | Reverse Primer |
gDNA | 1 | ISB_CA_AF | ISB_CA_AR.T1 |
NTC | 2 | ISB_CA_AF | ISB_CA_AR.T2 |
PCR Test[edit]
Components | 1X Volume | 2.5X Volume |
Captured template | 1 | 0 |
10uM Forward Primer | 0.4 | 1 |
10uM Reverse Primer | 0.4 | 0 |
2X KAPA SYBG MM | 12.5 | 31.25 |
H2O | 10.7 | 26.75 |
Total | 25 | 62.5 |
Program 98C 30s -> (98C 10s -> 52C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x21
File:2016-06-27 TB12kApr2016 V7 intubecapture testPCR.jpg
PCR[edit]
Components | 1X Volume | 2.5X Volume |
Captured template | 12 | 0 |
10uM Forward Primer | 2 | 5 |
10uM Reverse Primer | 2 | 0 |
2X KAPA SYBG MM | 50 | 125 |
H2O | 34 | 85 |
Total | 100 | 250 |
Program 98C 30s -> (98C 10s -> 52C 20s -> 72C 20s)x8 -> (98C 10s -> 72C 20s)x13 -> 72C 3min -> 4C hold
File:2016-06-27 TB12kApr2016 V7 intubecapture PCR.jpg
- Bead purification with 0.8:1 Beads to amplicon volume ratio
- Eluted with 50ul total for each sample
PAGE Check[edit]
File:2016-06-28 TB12kApr16V7 CapturegDNA.jpg
- Labeled tubes and put in "Non-quantified Sequencing Libraries"
- Sample: MC20160628_TB12kApr16V7_gDNA-1 (MC160628_TB12kAprV7_gDNA-1)