Author Archives: admin

Thursday 09/05/13

Posted on September 5, 2013 by admin

8:30a – 8:30p, 9:00p-11:50p Goals: Prep slides for meeting with XZ – complete. work on reply to reviewers – complete. Return Prob and Stats book – complete Set up splitdax analysis – running. book car for Banff – complete Themes … Continue reading →

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Wednesday 09/04/13

Posted on September 4, 2013 by admin

8:15a – 4:50p, 9:30p – 12:00a Discussions discuss project 2 troubleshooting with Hao and Jeff discuss with Jeff filtering STORM data on molecule properties (such as width photon number correlations or average intensity per flash as a function of space). … Continue reading →

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Protected: project 2: update 09/04/13

Posted on September 4, 2013 by admin

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Tuesday, 09/03/13

Posted on September 3, 2013 by admin

8:45a – 4:50p, 8:45p – 11:45p Goals re-read review — complete finish discussion — complete Stop IVT reaction, start RT reactions. Freeze RNA. — complete. talk to Hazen about fixing Hal. — fixed. call Calgary rental car. — Didn’t do. … Continue reading →

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Monday 09/02/13

Posted on September 2, 2013 by admin

8:30a – 6:00p, 8:00p – 11:10p T7 plate reaction planning (?) NEB Quick High Yield T7 template = 10 uL of T7 template (~30-120 ng/uL from spot check) 10 uL NTP buffer mix + 1uL (1/2x) T7 polII mix + … Continue reading →

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Sunday 09/01/13

Posted on September 1, 2013 by admin

8:00a – 11:00p Review working on incorporating feedback from Jeff into revision added new figure on explanation of Markov Models Cell staining goals: test probes from new library. Test Tye665 dye samples: Bxc-405 + Tye665 on clone8. Bxc-405 + cy5 … Continue reading →

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Saturday 08/31/13

Posted on August 31, 2013 by admin

8:00a – 5:30p, 10:20p – 10:50p Goals start incorporating feedback from Jeff into review Finish probe making for lib2 test samples. probe making see RT post for results Review feedback Explain thermodynamic models crucial part is that ‘probability of occupancy’ … Continue reading →

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RT reactions

Posted on August 30, 2013 by admin

background prep for RT reactions resuspended common-P1 at 1000 uM concentration 405 primer from Invitrogen not arrived yet compare superscriptII to superscriptIII in yield superscriptII protocol superscriptIII protocol 85 bp 1000 ng/uL ~ 35 pmol per uL = 350 pmol … Continue reading →

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Library analysis

Posted on August 30, 2013 by admin

Labeled version of gel: thoughts small sub-libraries preferentially lost? is this because we only get a fraction of the probes in each sublibrary to amplify? more likely a relative abundance issue — should have substantially more mass in large libraries. … Continue reading →

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Friday 08/30/13

Posted on August 30, 2013 by admin

8:30a-5:00p Goals for today RNA clean up of pilot Lib2 templates. comparison of SuperscriptII and SuperscriptIII RT yields plate scale in vitro transcription? Align multi-day stain get comments on review Coding writing script to aid finding cell matches from Mosaics … Continue reading →

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