Tag Archives: cell culture

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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Sunday 01/12/14

Posted on January 12, 2014 by admin

4:00p – 5:20p, 5:50p – 10:30p chromatin data analysis F03, F04, F05, and BX-C data does current spit dax work correctly on 512×256 images? Or are half the frames skipped? or something worse? seems to work just fine. Ran bead … Continue reading →

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Monday 11/25/13

Posted on November 25, 2013 by admin

9:10a – 11:45p Meetings Lab Meeting: private notes Journal Club: notes Mentoring Meeting Bogdan will explore length dependence in Blue domains BXC ~ 1900 nucleosomes — feasible scale for simulation Polymer simulations Bogdan attempting to get GPU accelerated openMM working … Continue reading →

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Friday 11/22/13

Posted on November 22, 2013 by admin

9:45a – 11:50a (remotely) 12:00p – 7:10p Genomics A549 whole cell data finished running cufflinks. Bottom half of genes are empty / all have zero FKPM (chr12 on). attempting to run cufflinks 2.1 centos6 version on cytosol BAM file directly … Continue reading →

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Thursday 11/14/13

Posted on November 14, 2013 by admin

9:30a – 11:45p Coding / Genomics Fixing fastaread to avoid memory errors Matlab calls char on the list of sequences. If there are short sequences and very long sequences mixed together in the fasta file, this can introduce many gigabytes … Continue reading →

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Saturday 11/02/13

Posted on November 2, 2013 by admin

9:00a – 12:00p remotely. 12:00p – 12:00a Goals Coding Add to ChromatinCropper export labeled overview fig, object centroid and bounding box in original coordinates (for computation of distance to lamina) direct measure of distance to lamina New functionalities for ChromatinCropper … Continue reading →

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Friday 11/01/13

Posted on November 1, 2013 by admin

10:00a – 9:15p Coding ChromatinCropper Current version not saving vlists! (molecule lists specific to ROI). need more display images in analysis. Data analysis: H:\2013-09-24_F6-405\splitdax Savefolder: ‘C:\Users\Alistair\Documents\Research\Projects\Chromatin\Data\2013-11-01_coloredRegions’ SplitDax System now checks filesize of the new daxfile. If expected size = actual … Continue reading →

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Tuesday 09/17/13

Posted on September 17, 2013 by admin

Library negative controls Get 10% bleach for spray bottle. Bleach all pipettes. Get all new tips 25 uL Phusion reactions 10 uM primer dilutions Fresh library 1:100 dilution 1 uL + 1.25 uL 10uM common Fresh library 1:100 dilution 1 … Continue reading →

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Thursday 08/29/13

Posted on August 29, 2013 by admin

8:15a – 7:00p Multi-stain analysis try crosslinking 415 beads to fresh, unfixed cells initial beads somewhat clumped and extremely bright, especially under high 405 illumination (or minimal weak 488 illumination). Beads do successfully blead into 647 channel at moderate brightness … Continue reading →

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Sunday 08/25/13

Posted on August 25, 2013 by admin

2:45p – 7:15p Review revising introduction of models Cell culture clone8 cells growing fast. A bit overgrown, need to split this afternoon. separated ‘non-adherent’ fraction of Kc167 cells remain primarily non-adherent. Adherent fraction of remains adherent. test plate Kc167 cells … Continue reading →

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