Tag Archives: chromatin

Monday 01/20/14

Posted on January 20, 2014 by admin

9:40a – 1:00a Goals send fig files to Jeff Upgrade memory on Cajal. Image ANT-C complex analyze black K100 (internal black domain) plots of internal vs. external. Lab Meeting see notes. journal club notes Computer stuff Memory installed on Cajal. … Continue reading →

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Saturday 01/18/2014

Posted on January 18, 2014 by admin

10:30a – 7:20p, matlab-storm STORMrender online Getting Jeff set up with STORMrender debugging: STORMfinder added paths in initialization, allowing matlab-storm to access depreciated versions of code in folders that weren’t supposed to be on filepath Features to add to STORMrender … Continue reading →

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Friday 01/17/14

Posted on January 17, 2014 by admin

11:50p – 12:45a, 2:00a – 3:20a (remotely) Chromatin Project Data analysis Goal: Sort data by expression levels. Getting FPKM expression values: Downloaded data from NCBI GEO database from the 25 Drosophila Cell lines paper. Downloading gene name conversion tables from … Continue reading →

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Thursday 01/16/2014

Posted on January 16, 2014 by admin

9:30a – 1:00a Happy Birthday. Goals Stain new cells: ANT-C, G05, D12 chromatin probe synthesis debugging order new Maxima and T7 create list of probes to make next start compressing bead data! – postponed again. Chromatin Project Finish O/N STORM … Continue reading →

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Tuesday 01/14/14

Posted on January 14, 2014 by admin

9:45a – 12:15a Goals Today Rewrite ColorIntervalJumpGap.m Function to allow different gaps for different chromatin types. Select new Red regions Chromatin Project analysis Designing some new regions: notes Writing up summary of chromatin regions thus far: see protected notes. Let’s … Continue reading →

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chromatin library organization and design

Posted on January 14, 2014 by admin

Introduction / Motivation Current library 3 design is still missing some key regions we would like to investigate very soon. For example there is no concerted attempt to bring red regions back into the fold. Preliminary observations of red regions … Continue reading →

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Monday 01/13/14

Posted on January 13, 2014 by admin

9:15a – 12:15a Plans for week probe making troubleshooting probe smears. Give Jeff some library material. make new probes (F01, F02, F07) + control + some of Jeff’s probes test different RNase inhibitors? Order Library 3 trim probe list (remove … Continue reading →

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Meeting XZ

Posted on January 13, 2014 by admin

Requests / timeline from XZ complete broad survey of regions before diving too deep on models hopefully one or two parameters can explain scaling between different regions naturally unsatisfying if a different / unrelated model is invoked for each scaling … Continue reading →

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Friday, 01/10/14

Posted on January 10, 2014 by admin

9:45a – 6:15p STORM imaging – multi-color chromatin O/N imaging of F5 F6 lost focus very early in night. O/N imaging buffer also did not survive well Re-imaging F11 F12 new freshly made Glox 2.5 uL BME + 5 uL … Continue reading →

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Thursday 01/09/14

Posted on January 9, 2014 by admin

9:50a – 5:30p, 10:00p – 12:15a Goals file reimbursement paperwork for post-doc visit check to Colenso for ski trip help Sebastian design probes chromatin project Run probe design for new chromatin regions selected to test off-diagonal HiC contacts Too many … Continue reading →

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