Monthly Archives: March 2013

Protected: lab meeting 03/25/13

Posted on March 25, 2013 by admin

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Sunday 03/24/13

Posted on March 24, 2013 by admin

11:00 A – 7:40 P Transcription modeling Failed to derive general case transcription rate for arbitrary number of transcriptionally competent states: Failed to derive probability density function for steady state distribution of mRNA transcripts (allowing for decay). Referee Complete, proofread … Continue reading →

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Saturday 03/23/13

Posted on March 23, 2013 by admin

11:00 A Cell culture Moved cell to 28C incubator observe substantial cell debris in dish (dead cells from heat shock?) Genomics Installing OligoArray2.0 http://berry.engin.umich.edu/oligoarray2/ Need to install legacy BLAST. Installed. Need to install OligoArrayAux: http://mfold.rna.albany.edu/?q=DINAMelt/OligoArrayAux. Error with database in2 = … Continue reading →

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Friday 03/22/13

Posted on March 22, 2013 by admin

11:00 A – 7:30 P, 9:30P – 11:58 P Discussion recommend using homology-fused single labeled probes to test the double labeling efficiency for Hao’s experiment. reference call for Bryon Genomics cleaned up Genomics functions maxInterval.m maxIntervalBed.m added new function IntervalFuseGaps.m … Continue reading →

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Saturday 03/16/13

Posted on March 16, 2013 by admin

11:00 A – 7:00P Kinetic modeling STORM Analysis Switching is indeed failing on BX-C 2/20 data. Sad we still don’t have this basic data with enough depth yet. S3 cell data shows plenty of blinking out at 58 and 90K … Continue reading →

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Friday 03/15/13

Posted on March 15, 2013 by admin

9:50 A – 8:30 P Goals Write SDB abstract. OligoPaint prep * Run probe design * Order probes 3. Chromatin color region selection * write script to chose genomic regions based on size, color, and color-confidence score. Genomics Probe Design … Continue reading →

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Thursday 03/14/13

Posted on March 14, 2013 by admin

10:00 A – 7:40P, 8:30P-10:30P Genomics processing real vanSteensel data now Reading in data and converting to int8 data matrix for data compression.cellfun(@(x) int8(round(20*str2double(x))), data) seems to be running slower than looping the over the columns… Actually need single to … Continue reading →

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Ethan Garner Seminar 03/14/13

Posted on March 14, 2013 by admin

lab running for ~6 months now. Introduction bacterial cell organization (in rod like cells): ends, middle, equally spaced ParM finds the ends by pushing — polymerizing until it starts bending. How bacteria grow cell wall holds shape. Digest this, get … Continue reading →

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Wednesday 03/13/13

Posted on March 13, 2013 by admin

10:00 A – 9:30P, 11:00P – 12:55 A STORM Finish O/N run on STORM2 STORM Analysis Launch Analysis of all fab7 data collected on STORM2 — now running on Cajal in small batches. Finish configuring local repo on TUCK to … Continue reading →

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multicolor by sequential staining

Posted on March 13, 2013 by admin

Approach Objective and Adventages Avoid some of the incompatiability issues of protein-DNA staining: Protein stains in previously untreated tissue should always work DNA stains should still work after protein imaging — it’s just the formamide treatment tends to kill the … Continue reading →

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