Tag Archives: coding

Protected: project2 update

Posted on March 5, 2014 by admin

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Wednesday 02/25/14

Posted on February 26, 2014 by admin

10:30a – 11:00p Chromatin Project Analysis Analysis of multi-color data quick look at G1-G2 data from 12-30. Almost complete overlap of regions. Current multi-color / adjacent region datasets: ‘Q:\2014-01-10_F11-7_F12-6’ ‘Q:\2014-01-10_G01-6_G02-7’ ‘Q:\2014-01-09_F05F06’ ‘Q:\2013-12-30_G1G2’ – 750 survived remarkably well. Should check buffer … Continue reading →

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Tuesday 02/25/14

Posted on February 25, 2014 by admin

11:00a – 11:30p Data compression (~11a-12p) troubleshooting beaddax averaging added some safety checks. System now checks to see if detected files for deletion contain the downsampled ds tag. If they do they won’t be deleted. System also checks if 561 … Continue reading →

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Friday 02/21/14

Posted on February 21, 2014 by admin

10:15a – 5:50p Chromatin Project Library 3 prep finish annotating new lib3 yellow green regions ran probe folding for yellow green regions Current probes (including 10 new black, 8 new blue): 91144 Deep Seq analysis Trying to understand why some … Continue reading →

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Thursday 02/13/14

Posted on February 13, 2014 by admin

9:30a – 12:40a Goals Today Start Bowtie analysis of Deep-Seq data Apply new drift correction approach to STORM data, compare spot quality STORM imaging of PH clusters + DNA FISH if anti-PH fails, try to restain with anti-Flag nuclear signal … Continue reading →

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Wednesday 02/12/14

Posted on February 12, 2014 by admin

9:50a – 11:59p Ph Project Cell staining hot wash post-hybe PBS wash Block 1 hour in 2% BSA primary stain rb a-Ph for 2 hrs RT, 6 hrs 4C rinse, wash in PBS, reblock, secondary stains O/N at 4C (m … Continue reading →

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Saturday 02/08/14

Posted on February 8, 2014 by admin

10:30a – 4:45p, 10:00p-11:50p Chromatin Deep sequencing of libraries finish gel extraction aborted last night due to mini-centrifuge failure. Data analysis Analyze new ANTP data issue: need to fix integrated drift correction, have some weird errors interpolation was not correct … Continue reading →

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Thursday 01/23/14

Posted on January 23, 2014 by admin

9:45a – 12:15a STORM analysis analyze bead data for BXC double stains analyze bead data for PhM Psc Finish O/N run of G05 quick look at ANTC data (just image based drift correction available at present) fewer localizations despite bright … Continue reading →

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Wednesday 01/15/14

Posted on January 15, 2014 by admin

9:30a – 12:30a Chromatin analysis loading Bogdan’s black area data. units or normalization is off somehow. These clearly don’t line up as expected. Redoing the spot-processing myself. Working on F1 data (very high background, this is a bit frustrating). F10 … Continue reading →

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Sunday 01/05/2014

Posted on January 5, 2014 by admin

10:30a – 8:00p, 10:00p-11:50p literature continue reading Berlivet et al PLoS Genetics on HoxA ID 19 candidate enhancers by ChIP and 5C 8 of 10 tested LacZ transgenics show limb bud enhancer activity TAD contacts in silent tissue Shh signalling … Continue reading →

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