Monthly Archives: October 2013

Wednesday 10/23/13

Posted on October 23, 2013 by admin

9:15a – Deep seq prep / discussion Miseq = 25M reads. Have almost 92K unique sequences in my library, so need 1M sequences just for 10 fold coverage. recommend run all libraries at equal concentration — we’ll get a lot … Continue reading →

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Tuesday 10/22/13

Posted on October 22, 2013 by admin

8:30a – 10:30p Goals Ph simulations: time and optimize? Ph simulations: add Ph-Flag species Analyze qPCR data chromatic warp computations for Bogdan Banff report RNA prep/ clean up RT reaction cast gels with Bogdan test RT reaction qPCR analysis for … Continue reading →

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Monday 10/21/13

Posted on October 21, 2013 by admin

10:40a – 12:00a Deep seq lib test gel clean up. 12 samples x 4 dilutions x 3 replicates = 144 samples dilution buffer = 10 mM Tris pH 8 + .05% Tween-20 (500 uL 1M Tris HCl + 250 10% … Continue reading →

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Sunday 10/20/13

Posted on October 19, 2013 by admin

1:00p-2:30p, 5:00p-11:50p Goals: Today write up some notes on Stowers presentations. layout slides for Rowland Center talk (in progress) This Week Write up Banff Report! Probe Making PCR: Large Regions (primer concentration) D11 100 kb percicentric Green (320 ng/uL) D12 … Continue reading →

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Wednesday 10/16/13

Posted on October 16, 2013 by admin

10:00am – 11:00pm Coding finishing up addition of cross-correlation based drift correction for global and local region data to ChromatinCropper GUI Mentoring Bogdan finds that samples which gave extra bands on PCR failed T7 reaction. Other samples gave good (~1000ng/uL) … Continue reading →

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Tuesday 10/15/13

Posted on October 15, 2013 by admin

11:00am – 12:30p Fly work Flip stocks terminate bottle stocks Coding working on ChromatinCropper added user controls added drift correction options changed display changed export / save data methods STORM STORM of G5-P2-Cy3 with G4-P1-405 Little/no signal in Cy3 channel … Continue reading →

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Monday 10/14/13

Posted on October 14, 2013 by admin

9:30a -12:30p STORM Analysis setting up more dot-finding analysis on Cajal setting up final splitQVdax for current data. Running stv2mat on all Mosaic data not yet processed. F10 seems to have issues running a complete round of splitQVdax. Some movies … Continue reading →

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Sunday 10/13/13

Posted on October 13, 2013 by admin

11:00a – 7:00p Ph Modeling chances = 0 if PhM >= PhWt This version finally gives the appropriate trend of clustering as a function of PhM concentration the tails are still too long, probably needs to be fixed by finite … Continue reading →

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Saturday 10/12/13

Posted on October 12, 2013 by admin

3:00p – 7:50p STORM Stop O/N STORM run of 475 kb black region F10 spot flickering not looks dimmer make new Glox test new hybes: G3/G4 failed. F12 failed. F9/G3 failed. Possible reasons for failure: suspect extended hot wash in … Continue reading →

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Friday 10/11/13

Posted on October 11, 2013 by admin

10:00a – 10:30p Goals send Ph modeling results to Ajaz work on presentation send reminder about racing Saturday STORM analysis Copying F11 data to ProBox2. Delete data from Storm2 Running splitdax on no405Primary, E07fail, F09, and F01v2 (latter 2 including … Continue reading →

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