Monthly Archives: April 2015

Thursday 04/09/15

Posted on April 16, 2015 by admin

9:00 am – 8:00 pm Ph project Figure making revising layout of Fig 5 sent to team NF says a bit too tight, need more whitespace. re-arranged panels again MERFISH exploring probe selection criteria compare variable length probes to 20mers … Continue reading →

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Wednesday, 04/15/15

Posted on April 15, 2015 by admin

9:00 am – 10:00 pm MERFISH Code development discuss Jeff’s new approach to Library construction Fix indexing in Assemble Oligo Array probes. complete. see Library11CompileOligoArrayResults_150414.m BLAST combos of primers and new Fast Secondaries completed for 5′ fusions. killed half of … Continue reading →

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Tuesday 04/14/15

Posted on April 14, 2015 by admin

10:00 am – 8:20 pm, 9:20pm – 12:00am MERFISH reply to Quake lab with raw data working on fixing lib12 build found bug in my matlab BLAST — allhits field not being populated if no varargin’s passed. fixed. updating MERFISH … Continue reading →

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SDB 2015 abstract

Posted on April 13, 2015 by admin

Super-resolution Imaging of Chromatin Nanostructure Links Epigenetic State and 3D Genome Packaging Metazoan genomes are packaged at multiple scales, and regulation of this spatial organization may play an important role in the developmental and cell fate selection. Unfortunately, current methods … Continue reading →

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Monday 04/13/15

Posted on April 13, 2015 by admin

9:00 am – 6:20 pm, 8:00 pm- 10:30 pm MERFISH design new libraries discussed design with team (9:30-10:30am) working on library assembly (8:00pm-10:00pm) New Libraries (140 gene). 20mer secondaries 30mer targeting regions 1-16 (shorter than before) 20mer secondaries 30mer targeting … Continue reading →

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Saturday 04/11/15

Posted on April 12, 2015 by admin

Ph Project working on simulations Assume certain amount of open sites. All will be fill with no Ph. Add PhM. The same fraction of PhM will be bound as the fraction of Ph bound, since the kinetics are the same. … Continue reading →

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Friday 04/10/15

Posted on April 10, 2015 by admin

10:00 am – 10:15 pm group meeting 10am-1pm MERFISH library design would like a new human transcriptome database, build off of multiple cell lines. Steven has ENCODE lines downloaded and cufflinks run. Just need to write matlab script to parse … Continue reading →

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MERFISH published! (in Science Magazine)

Posted on April 9, 2015 by admin

http://www.sciencemag.org/content/early/2015/04/08/science.aaa6090.abstract

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Wednesday 04/08/15

Posted on April 8, 2015 by admin

10:00 am – 8:00pm 10 am – 11 am: Ph simulations migrating Ph simulations onto Morgan. running Ph simulations maybe much shorter equilibration time and just many more rounds of simulation would be better running lots of short simulations across … Continue reading →

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Tuesday 04/07/15

Posted on April 7, 2015 by admin

9:00 am – 11:45 pm Tasks revise Text for chromatin paper Extended data figures for chromatin entanglement (done) revise Fig 4 Histone images for Doory (sent) Revised model figure for Ajaz write abstract for ASBMB on MERFISH (see post) write … Continue reading →

Posted in Summaries | Comments Off on Tuesday 04/07/15