Monthly Archives: January 2014

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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Protected: Library 2 results summary so far

Posted on January 16, 2014 by admin

There is no excerpt because this is a protected post.

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Protected: chromatin snapshots 01/15/14

Posted on January 16, 2014 by admin

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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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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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Protected: Survey summary, Library 2 chromatin data

Posted on January 14, 2014 by admin

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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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