Tag Archives: Library2

Protected: Library 2 results summary so far

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Wednesday 01/15/14

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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chromatin library organization and design

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

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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Sunday 01/12/14

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 11/11/13

8:40a – 1:15a Ph project Get S2 cells for Ajaz Running more simulations to explore appropriate range and parameters for the effect of PhM concentration on clustering. For the moment let’s ignore the unbound populations of molecules. Surprisingly I observe … Continue reading

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Saturday 11/09/13

8:30a – 7:30p, 8:30p – 11:30p (remotely) Goals Write to Alvaro (done) Reply to Zenklusen (done) Continue analysis of MiSeq Results (in process) write to Jeff to get gene list (done) repeat RT reaction with more enzyme (done) Work on … Continue reading

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Thursday 10/07/13

9:25a – 11:50p Probe Making very poor probe incorporation. Maybe the lower concentration of Maxima? Try to run RT again tomorrow to compare. attempted DCC of probes to remove excess primer using short probes 1-4. Extremely low yield (20 ng/uL … Continue reading

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Wednesday 11/06/13

8:30a – 12:20a Morning tasks give Jeff deep-seq prep’d sample 4 (F3) to run as qPCR standard All analysis tasks on Cajal and all split-dax running from Monet completed. Restart Monet to install new 4Tb HDs: ProBox5 & 6. Move … Continue reading

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Monday 11/04/13

8:40a – 12:50a Goals Cell culture check cells. Probably all need to grow at least another day or two Show BB the contaminated cultures for teachable moment. Cell staining ~ 3-4 pm start hot washes for Y RNA vs DNA … Continue reading

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