Tag Archives: troubleshooting

Thursday 12/12/13

Posted on December 12, 2013 by admin

10:45a – 11:00p Ph Simulations Troubleshooting extra along bonds. Oops, actually just resulted from plotting the wrong attachment matrix for the given position list. Simulations ran at subsaturating Ph — more total sites than available Ph. Hence there is a … Continue reading →

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denaturing diagnostic gels

Posted on April 14, 2013 by admin

Gel 1, 5% Agarose, 200 V in sodium-Borax (300 V melts gel). Gel 2, 15% Urea, 120V 2 hrs Gel 3 15% Urea gel, 120 V 50 min in 37C room Gel 4, 10% precast Urea denaturing gel, 120 V, … Continue reading →

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Thursday 04/11/13

Posted on April 11, 2013 by admin

Oligo Paint Probe synthesis Test PCRs at 1 mL scale: Assymetric y-PCR, Y-adapter, no Y-L primer + 1uL of EtOH extracted Y PCR product at 85 ng/uL Assymetric b-PCR, B-adapter + 1 uL of EtOH extracted B PCR product at … Continue reading →

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Protected: Activator oligoPaints: results summary 04/05/13

Posted on April 5, 2013 by admin

There is no excerpt because this is a protected post.

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Protected: issues with ph-FLAG round 1

Posted on April 5, 2013 by admin

There is no excerpt because this is a protected post.

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oligopaint-PCR

Posted on April 4, 2013 by admin

Calculating concentrations (Qubit) and molecule numbers: starting primer = 30 ng in 300 uL in 1 ng/uL, added 100 uL = 100 ng 100 uM = 100E-12 mols/uL add 100 uL, = 10 nmols starting primer. Y PCR: 73.7 ng/mL … Continue reading →

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Tuesday 03/05/13

Posted on March 5, 2013 by admin

9:50 A – 7:30 P, 8:30 P – 10:50 P General Discussing replies for Banff invites. Student substitutions add to bottom of list Still need to write more acknowledgement of replies. STORM Analysis launch analysis of all unprocessed datafiles. ESATA … Continue reading →

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embryo sections

Posted on March 5, 2013 by admin

some sections lie nice and flat, others get substantial ripples. Is this knife compression? too large a section in x-y? (seems to correlate). Too thick a section? (seems also to be true in my experience).

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Z-calibration part 2

Posted on February 4, 2013 by admin

Curves fit the following polynomial: $latex w_x=\sqrt{w_{x0} \sqrt{B_xX^4+A_xX^3+X^2+1}}$ where $latex X= (z-g_x)/(z_{rx})$ In general we will require $latex gx$ to be negative $latex gy$ to be positive. $latex Ax$ and $latex Bx$ are correction factors and should be small. See … Continue reading →

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issues with non-blinking weak spots

Posted on November 15, 2012 by admin

The very bright, round foci clearly do not correspond to objects in the conventional image and are probably all artificats from non-switching foci. These dots start off at moderate single molecule brightness (can’t eliminate them just using higher threshold cutoff … Continue reading →

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