Daniel:Notebook/ComboLock/2016-12-15: Difference between revisions
>Djacobse |
>Djacobse |
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(11 intermediate revisions by the same user not shown) | |||
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<li>Rinse gel and image in gel doc</li> | <li>Rinse gel and image in gel doc</li> | ||
</ol></ol> | </ol></ol> | ||
===Results=== | |||
<gallery perrow=3 heights=300px widths=300px> | |||
File:20161215-qPCR-MirrorCProbes-Adapters-SamplevsControl-Beads.png|qPCR curve displaying sample vs C probes (for supernatant) | |||
File:20161215-qPCR-MirrorCProbes-Adapters-SamplevsControl.png|qPCR curve displaying sample vs C probes (for beads) | |||
File:20161215-qPCR-MirrorCProbes-Adapters-SupvsBeads.png|qPCR curve displaying supernatant vs. beads effect | |||
File:2016-12-15-MirrorCProbe-Adapters-CProbeDetection.png|Gel image 1-Sample C probe detection | |||
File:2016-12-15-MirrorCProbe-Adapters-Controls.png|Gel image 2-Controls gel | |||
</gallery> | |||
===qPCR Sample Matrix=== | ===qPCR Sample Matrix=== | ||
Line 316: | Line 326: | ||
| width="100" height="45" | Sample | | width="100" height="45" | Sample | ||
| width="120" | Condition | | width="120" | Condition | ||
| width=" | | width="90" | Primers | ||
| width="130" | Primer Target | | width="130" | Primer Target | ||
| width=" | | width="91" | Fraction | ||
| width="65" | Lane | | width="65" | Lane | ||
| width="65" | Sample Vol (uL) | | width="65" | Sample Vol (uL) | ||
| width="73" | 2X Kapa SYBR qPCR MM | | width="73" | 2X Kapa SYBR qPCR MM | ||
| width=" | | width="80" | 10 uM Forward Primer | ||
| width=" | | width="80" | 10 uM Reverse Primer | ||
| width="65" | H2O | | width="65" | H2O | ||
| width="65" | Total Volume (uL) | | width="65" | Total Volume (uL) | ||
| width="65" | Master Mix | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 335: | Line 345: | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | A1 | | align="center" | A1 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 342: | Line 351: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
Line 350: | Line 360: | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | A2 | | align="center" | A2 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 357: | Line 366: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 365: | Line 375: | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | A3 | | align="center" | A3 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 372: | Line 381: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
Line 380: | Line 390: | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | A4 | | align="center" | A4 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 387: | Line 396: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 394: | Line 404: | ||
| align="center" | Circular Product | | align="center" | Circular Product | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | | | align="center" | A5 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 402: | Line 411: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |- style="background-color:#BFBFBF;font-size:12pt" | ||
Line 409: | Line 419: | ||
| align="center" | Circular Product | | align="center" | Circular Product | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | | | align="center" | A6 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 417: | Line 426: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 424: | Line 434: | ||
| align="center" | C1 | | align="center" | C1 | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | C1 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 432: | Line 441: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="background-color:#DA9694;font-size:12pt" | |- style="background-color:#DA9694;font-size:12pt" | ||
Line 439: | Line 449: | ||
| align="center" | C1 | | align="center" | C1 | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | C2 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 447: | Line 456: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 454: | Line 464: | ||
| align="center" | C2 | | align="center" | C2 | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | C3 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 462: | Line 471: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="background-color:#DA9694;font-size:12pt" | |- style="background-color:#DA9694;font-size:12pt" | ||
Line 469: | Line 479: | ||
| align="center" | C2 | | align="center" | C2 | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | C4 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 477: | Line 486: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 484: | Line 494: | ||
| align="center" | Circular Product | | align="center" | Circular Product | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | C5 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 492: | Line 501: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|- style="background-color:#DA9694;font-size:12pt" | |- style="background-color:#DA9694;font-size:12pt" | ||
Line 499: | Line 509: | ||
| align="center" | Circular Product | | align="center" | Circular Product | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | C6 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 507: | Line 516: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 514: | Line 524: | ||
| align="center" | C1 | | align="center" | C1 | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | | | align="center" | F1 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 522: | Line 531: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="background-color:#C4D79B;font-size:12pt" | |- style="background-color:#C4D79B;font-size:12pt" | ||
Line 529: | Line 539: | ||
| align="center" | C1 | | align="center" | C1 | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | | | align="center" | F2 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 537: | Line 546: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 544: | Line 554: | ||
| align="center" | C2 | | align="center" | C2 | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | | | align="center" | F3 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 552: | Line 561: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="background-color:#C4D79B;font-size:12pt" | |- style="background-color:#C4D79B;font-size:12pt" | ||
Line 559: | Line 569: | ||
| align="center" | C2 | | align="center" | C2 | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | | | align="center" | F4 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 567: | Line 576: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 574: | Line 584: | ||
| align="center" | Circular Product | | align="center" | Circular Product | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | | | align="center" | F5 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 582: | Line 591: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|- style="background-color:#C4D79B;font-size:12pt" | |- style="background-color:#C4D79B;font-size:12pt" | ||
Line 589: | Line 599: | ||
| align="center" | Circular Product | | align="center" | Circular Product | ||
| align="center" | Supernatant-PreRCA | | align="center" | Supernatant-PreRCA | ||
| align="center" | | | align="center" | F6 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 597: | Line 606: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 604: | Line 614: | ||
| align="center" | C1 | | align="center" | C1 | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | H1 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 612: | Line 621: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="background-color:#B1A0C7;font-size:12pt" | |- style="background-color:#B1A0C7;font-size:12pt" | ||
Line 619: | Line 629: | ||
| align="center" | C1 | | align="center" | C1 | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | H2 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 627: | Line 636: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 634: | Line 644: | ||
| align="center" | C2 | | align="center" | C2 | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | H3 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 642: | Line 651: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="background-color:#B1A0C7;font-size:12pt" | |- style="background-color:#B1A0C7;font-size:12pt" | ||
Line 649: | Line 659: | ||
| align="center" | C2 | | align="center" | C2 | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | H4 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 657: | Line 666: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 664: | Line 674: | ||
| align="center" | Circular Product | | align="center" | Circular Product | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | H5 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 672: | Line 681: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|- style="background-color:#B1A0C7;font-size:12pt" | |- style="background-color:#B1A0C7;font-size:12pt" | ||
Line 679: | Line 689: | ||
| align="center" | Circular Product | | align="center" | Circular Product | ||
| align="center" | Beads-PreRCA | | align="center" | Beads-PreRCA | ||
| align="center" | | | align="center" | H6 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 687: | Line 696: | ||
| align="center" align="center" | 21 | | align="center" align="center" | 21 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 695: | Line 705: | ||
| align="center" valign="bottom" | NA | | align="center" valign="bottom" | NA | ||
| align="center" | A7 | | align="center" | A7 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 702: | Line 711: | ||
| align="center" align="center" | 23 | | align="center" align="center" | 23 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC1 | |||
|- style="background-color:#FABF8F;font-size:12pt" | |- style="background-color:#FABF8F;font-size:12pt" | ||
Line 709: | Line 719: | ||
| align="center" valign="bottom" | C2 | | align="center" valign="bottom" | C2 | ||
| align="center" valign="bottom" | NA | | align="center" valign="bottom" | NA | ||
| align="center" | | | align="center" | C7 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 717: | Line 726: | ||
| align="center" align="center" | 23 | | align="center" align="center" | 23 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMC2 | |||
|- style="font-size:12pt" | |- style="font-size:12pt" | ||
Line 724: | Line 734: | ||
| align="center" valign="bottom" | Circular Product | | align="center" valign="bottom" | Circular Product | ||
| align="center" valign="bottom" | NA | | align="center" valign="bottom" | NA | ||
| align="center" | | | align="center" | F7 | ||
| align="center" align="center" | 2 | | align="center" align="center" | 2 | ||
| align="center" align="center" | 25 | | align="center" align="center" | 25 | ||
Line 732: | Line 741: | ||
| align="center" align="center" | 23 | | align="center" align="center" | 23 | ||
| align="center" align="center" | 50 | | align="center" align="center" | 50 | ||
| align="center" | MMCP | |||
|} | |||
=Overnight Capture= | |||
So based on the results above, I'd say that the latch and padlock are not both finding their targets at the same time, which is leading to a situation where nothing works. So I'm going to repeat the experiment but with an overnight capture step that will give everything time to settle. I'll incubate at 60C overnight for capture (The Tm of the adapters is designed to 65 btw). Tomorrow I will add the phusion reaction (Phusion polymerase + Amp Ligase) for 2 hours without taking the samples off the incubator. | |||
==Sample Matrix== | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="background-color:#CCC0DA;font-size:12pt;font-weight:bold" align="center" | |||
| width="150" height="34" | Sample | |||
| width="120" | Condition | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Sample 1 (AB) | |||
| align="center" valign="bottom" | Normal | |||
|- style="background-color:#BFBFBF;font-size:12pt" | |||
| height="15" valign="bottom" | Sample 2 (AB) | |||
| align="center" valign="bottom" | No Template | |||
|- style="font-size:12pt" | |||
| height="15" valign="bottom" | Sample 3 (AB) | |||
| align="center" valign="bottom" | No C probes | |||
|} | |} | ||
==Protocol== | |||
<ol> | |||
<li>Template-Bead Binding</li> | |||
<ol type="A"> | |||
<li>Suspend 2 uL (8 ug) beads per sample in 100 uL wash buffer </li> | |||
<li>Apply magnet for 30 sec and remove supernatant</li> | |||
<li>Add 2 uL 10 uM template oligo per sample to bead solution; incubate at RT for 5 min</li> | |||
<li>Wash beads with 100 uL wash buffer; vortex to suspend; apply magnet and remove supernatant</li> | |||
</ol> | |||
<li>C Probe Hybridization</li> | |||
<ol type="A"> | |||
<li>Combine 1 uL of each C probe (10 uM stock) and 3 uL bead wash buffer into a 0.2 mL tube</li> | |||
<li>Heat C probes to 90C for 5 min; Chill probes on ice to quench</li> | |||
<li>Add 5 uL probe mixture to beads</li> | |||
<li>Incubate at 40C for 1 hour with agitation</li> | |||
<li>Wash beads with 100 uL wash buffer; apply magnet and remove supernatant</li> | |||
<li>Repeat wash step above</li> | |||
<li>Add 100 uL cold Low Salt Buffer; apply magnet and remove supernatant</li> | |||
</ol> | |||
<li>Latch and Padlock Hybridization</li> | |||
<ol type="A"> | |||
<li>Add following to a fresh 0.2 mL tube</li> | |||
<ol type="a"> | |||
<li>12.2 uL Latch0001, 10 uM stock</li> | |||
<li>12.2 uL Padlock0201, 10 uM stock</li> | |||
<li>12.2 uL Amp10X buffer</li> | |||
<li>85.4 uL nfH2O</li></ol> | |||
<li>Incubate at 60C overnight</li></ol> | |||
Continued [[Daniel:Notebook/ComboLock/2016-12-16|tomorrow]] | |||
[[Category:ComboLock]] [[Category:20161213]] [[Category:20161215]] |
Latest revision as of 17:51, 16 December 2016
Mirror Probe Test (Started Tuesday)[edit]
RCA on Beads/Supernatant Fractions[edit]
- qPCR
- Make master mix according to following recipe
- 298.2 uL nfH2O
- 355 uL SYBR Fast
- 14.2 uL 10 uM AmpF
- Add 47 uL master mix to each well
- Add 2 uL sample and 1 uL appropriate Reverse Primer (1 uM) according to table in the following section
- qPCR Cycles
- 95C 3 min
- 95C 3 sec
- 55C 30 sec
- 72C 20 sec
- plate read
- goto b x24
- 72C 2 min
- 16C hold
- TBE Gel
- Mix 144 uL TBE, 36 uL 6x loading dye
- Aliquot 10 uL per sample/ladder lane onto parafilm
- Add 2 uL of sample or ladder to correct drop
- Load 10 uL in to well
- Run gel for 22 minutes at 250V
- Open gel and stain with 3 uL SYBR Gold for 3 minutes
- Rinse gel and image in gel doc
Sample | Condition | Fraction | Lane | AmpR Index | Sample Vol (uL) | 2X Kapa SYBR qPCR MM | 10 uM Forward Primer | 10 uM Reverse Primer | H2O | Total Volume (uL) |
Sample 1A | Sample | Supernatant | A1 | 20 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 1B | Sample | Supernatant | A2 | 20 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 2A | No Template | Supernatant | A3 | 21 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 2B | No Template | Supernatant | A4 | 21 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 3A | No C Probe | Supernatant | A5 | 22 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 3B | No C Probe | Supernatant | A6 | 22 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 1A | Sample | Beads | H1 | 23 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 1B | Sample | Beads | H2 | 23 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 2A | No Template | Beads | H3 | 24 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 2B | No Template | Beads | H4 | 24 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 3A | No C Probe | Beads | H5 | 25 | 2 | 25 | 1 | 1 | 21 | 50 |
Sample 3B | No C Probe | Beads | H6 | 25 | 2 | 25 | 1 | 1 | 21 | 50 |
NTC | qPCR Primers Only | NA | A7 | 26 | 2 | 25 | 1 | 1 | 23 | 50 |
Results[edit]
- 20161215-qPCR-MirrorCProbe-PostRCA.png
qPCR curves
- 2016-12-15-MirrorCProbe-RCA-Supernatant.png
Gel image-supernatant RCA
- 2016-12-15-MirrorCProbe-RCA-Beads.png
Gel image-beads RCA
Although there is a slight smear in the region of correct size (211bp), the smear is present in every lane (except the NTC). This suggests the smear is a result of the beads in general and not really related to the product. My conclusion is that the circular product never formed.
C Probe and Product Detection[edit]
I'm now going to investigate the presence/absence of C probes and circularized products using the adapter primers.
- qPCR
- Make master mix according to following recipes
- Add 48 uL master mix to each well
- Add 2 uL sample according to table in the following section
- qPCR Cycles
- 95C 3 min
- 95C 3 sec
- 55C 30 sec
- 72C 20 sec
- plate read
- goto b x24
- 72C 2 min
- 16C hold
- TBE Gel
- Mix 144 uL TBE, 36 uL 6x loading dye
- Aliquot 10 uL per sample/ladder lane onto parafilm
- Add 2 uL of sample or ladder to correct drop
- Load 10 uL in to well
- Run gel for 22 minutes at 250V
- Open gel and stain with 3 uL SYBR Gold for 3 minutes
- Rinse gel and image in gel doc
Master Mix | Primers | Primer Target | 2X Kapa SYBR qPCR MM | 10 uM Forward Primer | 10 uM Reverse Primer | H2O | Master Mix |
MMC1 | p24/p4* | C1 | 230 | 9.2 | 9.2 | 193.2 | MMC1 |
MMC2 | p24/p4* | C1 | 230 | 9.2 | 9.2 | 193.2 | MMC1 |
MMCP | p6/p12* | C2 | 230 | 9.2 | 9.2 | 193.2 | MMC2 |
Results[edit]
- 20161215-qPCR-MirrorCProbes-Adapters-SamplevsControl-Beads.png
qPCR curve displaying sample vs C probes (for supernatant)
- 20161215-qPCR-MirrorCProbes-Adapters-SamplevsControl.png
qPCR curve displaying sample vs C probes (for beads)
- 20161215-qPCR-MirrorCProbes-Adapters-SupvsBeads.png
qPCR curve displaying supernatant vs. beads effect
- 2016-12-15-MirrorCProbe-Adapters-CProbeDetection.png
Gel image 1-Sample C probe detection
- 2016-12-15-MirrorCProbe-Adapters-Controls.png
Gel image 2-Controls gel
qPCR Sample Matrix[edit]
Sample | Condition | Primers | Primer Target | Fraction | Lane | Sample Vol (uL) | 2X Kapa SYBR qPCR MM | 10 uM Forward Primer | 10 uM Reverse Primer | H2O | Total Volume (uL) | Master Mix |
Sample 1A | Sample | p24/p4* | C1 | Supernatant-PreRCA | A1 | 2 | 25 | 1 | 1 | 21 | 50 | MMC1 |
Sample 1B | Sample | p24/p4* | C1 | Supernatant-PreRCA | A2 | 2 | 25 | 1 | 1 | 21 | 50 | MMC1 |
Sample 1A | Sample | p6/p12* | C2 | Supernatant-PreRCA | A3 | 2 | 25 | 1 | 1 | 21 | 50 | MMC2 |
Sample 1B | Sample | p6/p12* | C2 | Supernatant-PreRCA | A4 | 2 | 25 | 1 | 1 | 21 | 50 | MMC2 |
Sample 1A | Sample | p24/p12* | Circular Product | Supernatant-PreRCA | A5 | 2 | 25 | 1 | 1 | 21 | 50 | MMCP |
Sample 1B | Sample | p24/p12* | Circular Product | Supernatant-PreRCA | A6 | 2 | 25 | 1 | 1 | 21 | 50 | MMCP |
Sample 1A | Sample | p24/p4* | C1 | Beads-PreRCA | C1 | 2 | 25 | 1 | 1 | 21 | 50 | MMC1 |
Sample 1B | Sample | p24/p4* | C1 | Beads-PreRCA | C2 | 2 | 25 | 1 | 1 | 21 | 50 | MMC1 |
Sample 1A | Sample | p6/p12* | C2 | Beads-PreRCA | C3 | 2 | 25 | 1 | 1 | 21 | 50 | MMC2 |
Sample 1B | Sample | p6/p12* | C2 | Beads-PreRCA | C4 | 2 | 25 | 1 | 1 | 21 | 50 | MMC2 |
Sample 1A | Sample | p24/p12* | Circular Product | Beads-PreRCA | C5 | 2 | 25 | 1 | 1 | 21 | 50 | MMCP |
Sample 1B | Sample | p24/p12* | Circular Product | Beads-PreRCA | C6 | 2 | 25 | 1 | 1 | 21 | 50 | MMCP |
Sample 3A | No C Probes | p24/p4* | C1 | Supernatant-PreRCA | F1 | 2 | 25 | 1 | 1 | 21 | 50 | MMC1 |
Sample 3B | No C Probes | p24/p4* | C1 | Supernatant-PreRCA | F2 | 2 | 25 | 1 | 1 | 21 | 50 | MMC1 |
Sample 3A | No C Probes | p6/p12* | C2 | Supernatant-PreRCA | F3 | 2 | 25 | 1 | 1 | 21 | 50 | MMC2 |
Sample 3B | No C Probes | p6/p12* | C2 | Supernatant-PreRCA | F4 | 2 | 25 | 1 | 1 | 21 | 50 | MMC2 |
Sample 3A | No C Probes | p24/p12* | Circular Product | Supernatant-PreRCA | F5 | 2 | 25 | 1 | 1 | 21 | 50 | MMCP |
Sample 3B | No C Probes | p24/p12* | Circular Product | Supernatant-PreRCA | F6 | 2 | 25 | 1 | 1 | 21 | 50 | MMCP |
Sample 3A | No C Probes | p24/p4* | C1 | Beads-PreRCA | H1 | 2 | 25 | 1 | 1 | 21 | 50 | MMC1 |
Sample 3B | No C Probes | p24/p4* | C1 | Beads-PreRCA | H2 | 2 | 25 | 1 | 1 | 21 | 50 | MMC1 |
Sample 3A | No C Probes | p6/p12* | C2 | Beads-PreRCA | H3 | 2 | 25 | 1 | 1 | 21 | 50 | MMC2 |
Sample 3B | No C Probes | p6/p12* | C2 | Beads-PreRCA | H4 | 2 | 25 | 1 | 1 | 21 | 50 | MMC2 |
Sample 3A | No C Probes | p24/p12* | Circular Product | Beads-PreRCA | H5 | 2 | 25 | 1 | 1 | 21 | 50 | MMCP |
Sample 3B | No C Probes | p24/p12* | Circular Product | Beads-PreRCA | H6 | 2 | 25 | 1 | 1 | 21 | 50 | MMCP |
NTC | qPCR Primers Only | p24/p4* | C1 | NA | A7 | 2 | 25 | 1 | 1 | 23 | 50 | MMC1 |
NTC | qPCR Primers Only | p6/p12* | C2 | NA | C7 | 2 | 25 | 1 | 1 | 23 | 50 | MMC2 |
NTC | qPCR Primers Only | p24/p12* | Circular Product | NA | F7 | 2 | 25 | 1 | 1 | 23 | 50 | MMCP |
Overnight Capture[edit]
So based on the results above, I'd say that the latch and padlock are not both finding their targets at the same time, which is leading to a situation where nothing works. So I'm going to repeat the experiment but with an overnight capture step that will give everything time to settle. I'll incubate at 60C overnight for capture (The Tm of the adapters is designed to 65 btw). Tomorrow I will add the phusion reaction (Phusion polymerase + Amp Ligase) for 2 hours without taking the samples off the incubator.
Sample Matrix[edit]
Sample | Condition |
Sample 1 (AB) | Normal |
Sample 2 (AB) | No Template |
Sample 3 (AB) | No C probes |
Protocol[edit]
- Template-Bead Binding
- Suspend 2 uL (8 ug) beads per sample in 100 uL wash buffer
- Apply magnet for 30 sec and remove supernatant
- Add 2 uL 10 uM template oligo per sample to bead solution; incubate at RT for 5 min
- Wash beads with 100 uL wash buffer; vortex to suspend; apply magnet and remove supernatant
- C Probe Hybridization
- Combine 1 uL of each C probe (10 uM stock) and 3 uL bead wash buffer into a 0.2 mL tube
- Heat C probes to 90C for 5 min; Chill probes on ice to quench
- Add 5 uL probe mixture to beads
- Incubate at 40C for 1 hour with agitation
- Wash beads with 100 uL wash buffer; apply magnet and remove supernatant
- Repeat wash step above
- Add 100 uL cold Low Salt Buffer; apply magnet and remove supernatant
- Latch and Padlock Hybridization
- Add following to a fresh 0.2 mL tube
- 12.2 uL Latch0001, 10 uM stock
- 12.2 uL Padlock0201, 10 uM stock
- 12.2 uL Amp10X buffer
- 85.4 uL nfH2O
- Incubate at 60C overnight
Continued tomorrow