Author Archives: admin

Saturday 10/26/13

Posted on October 26, 2013 by admin

10:00a – 8:00p Banff report (working remotely) Trimming scientific progress section (whole report needs to fit in 4 pages) added more participant comments into all sections (I think this is more meaningful the organizer summaries). STORM4 Record chromatic bead data. … Continue reading →

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Friday 10/25/13

Posted on October 25, 2013 by admin

10:00a – 9:00p Ph Meeting (10:30-1:00p) More numbers simple fig for on rate / off rate model descrimination need more bio-info trends Psc knockdown Mentoring Discussing Random Walk simulation algorithms explaining existing model code presented stripped down model code for … Continue reading →

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Thursday 10/24/13

Posted on October 24, 2013 by admin

8:40a – 6:20p, 11:30p – 12:55a Goals Fix Ph model — neigbhors of neighbors in situs day 2 Cell Staining Hot washes (20 min, 2x 9 min in oven + 1 min switch) 1x SSCT cold wash PBT wash 45 … Continue reading →

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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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