Author Archives: admin

Saturday 08/08/15

Posted on August 8, 2015 by admin

11:00 am – 1:15 am PcG RNAi New Knockdowns and cell culture plate Ph, Pc, and mock RNAi cells onto coverglass density looks okay modulo a decent number aren’t sticking isolated cells for RNA extraction fixed plated cells to coverglass … Continue reading →

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Thursday 08/06/15

Posted on August 6, 2015 by admin

10:00 am – 11:00 pm To do PRE correlation analysis expression correlation analysis design and Green domain probes finish updates to ChromatinCropper2 analyze internal domain data Correlation analyses repeated PRE analysis as discussed: recomputed using Cavalli/Tanay labs latest PRE predictions … Continue reading →

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Wednesday 08/05/15

Posted on August 5, 2015 by admin

9:00 am – 12:00 am STORM live imaging construct doesn’t show expected pattern fixed issue with 561 power (half-wave-plate was turned) so the beam entered the polarizing beam-splitter the wrong way. STORM Ph-KD imaging imaging Ph-KD L2F04 sample seems to … Continue reading →

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Tuesday 08/04/15

Posted on August 4, 2015 by admin

9:45 am – 11:15 pm Batch data analysis of confocal live imaging of fixation effects Matched feature aligned images: Positive Control: A few more examples of positive control Signed up for Elyra training MERFISH analyzing L12 data see notebook post … Continue reading →

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Monday 08/03/15

Posted on August 3, 2015 by admin

9:15 am – 5:05 pm, Goals chromatin STORM finish STORM session of L2F03 dat in Ph-KD condition take bead movies, transfer data start fitting movies after transfer completes setup auto-transfer (?) for next time Ph project send Ph data on … Continue reading →

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Exploring Fixation Effects 08/03/15

Posted on August 3, 2015 by admin

Confocal images of live and fixed cells with different fixation methods Using automated image processing to ID effects on chromatin structure. Time control MEOH fixed sample Experiment vs Negative control Switched from simple rescaling to feature finding using FIJI / … Continue reading →

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Sunday 08/02/15

Posted on August 2, 2015 by admin

11:00 am – 3:30 pm, 6:30 pm – 11:15 pm STORM STORM2 froze during the night (click error provided an out of frame crash in python — built in check doesn’t catch it. debugged this with Bogdan, changed catch statement … Continue reading →

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Friday 07/31/15

Posted on July 31, 2015 by admin

9:00 am – 5:00 pm Lab meeting see notes Discussion talk with Ting talk with Xiaowei chromatin project project update meeting see google-docs slides Ph Project need to downsample localizations (2-fold?) an re-compute statistics and show similar distribution.

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Thur 07/30/15

Posted on July 31, 2015 by admin

11:00 am – 7:30 pm, 9:30 pm – 10:45 pm (9:00 am – 11:00 am volleyball practice) Chromatin Cell plated Kc167 cells (in SFX) on glass my more recent flask with the short Trypsin treatment is doing well. the original … Continue reading →

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Protected: lab meeting: 07/31/15

Posted on July 31, 2015 by admin

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