Tag Archives: probe making

Saturday 08/31/13

Posted on August 31, 2013 by admin

8:00a – 5:30p, 10:20p – 10:50p Goals start incorporating feedback from Jeff into review Finish probe making for lib2 test samples. probe making see RT post for results Review feedback Explain thermodynamic models crucial part is that ‘probability of occupancy’ … Continue reading →

Posted in Summaries | Tagged | Comments Off on Saturday 08/31/13

RT reactions

Posted on August 30, 2013 by admin

background prep for RT reactions resuspended common-P1 at 1000 uM concentration 405 primer from Invitrogen not arrived yet compare superscriptII to superscriptIII in yield superscriptII protocol superscriptIII protocol 85 bp 1000 ng/uL ~ 35 pmol per uL = 350 pmol … Continue reading →

Posted in probe and plasmid building | Tagged , | Comments Off on RT reactions

Friday 08/30/13

Posted on August 30, 2013 by admin

8:30a-5:00p Goals for today RNA clean up of pilot Lib2 templates. comparison of SuperscriptII and SuperscriptIII RT yields plate scale in vitro transcription? Align multi-day stain get comments on review Coding writing script to aid finding cell matches from Mosaics … Continue reading →

Posted in probe and plasmid building, Summaries | Tagged , , | Comments Off on Friday 08/30/13

plate PCR for 82 libraries

Posted on August 28, 2013 by admin

for each sublib (50 uL reaction) 19 ddH2O 5 uL 5 uM common 1 uL of 1:10 diluted library 25 uL Phusion master 0.25 uL of 200 uM T7 lib specific primer master mix (83x) 1577 uL ddH2O 415 uL … Continue reading →

Posted in probe and plasmid building | Tagged , | Comments Off on plate PCR for 82 libraries

T7 in vitro Tx

Posted on August 28, 2013 by admin

Library2, samples G1-8 skip sample G1, no DNA recovery NEB For each sub-library, mix the following in a single PCR tube or well of a PCR strip or plate 8 uL DNA template + 2uL ddH2o 1.5 uL 10X T7 … Continue reading →

Posted in probe and plasmid building | Tagged , | Comments Off on T7 in vitro Tx

PCR

Posted on August 28, 2013 by admin

Amplifying G1-8 using T7 primers for each sublib 18.5 ddH2O 5 uL 5uM common 1 uL library (cut to .5, at 1uL I can only do each lib once) 25 uL Phusion master master mix (9x) 166.5 uL ddH2O 45 … Continue reading →

Posted in probe and plasmid building, Summaries | Tagged , | Comments Off on PCR

Monday 08/26/13

Posted on August 26, 2013 by admin

9:45a – 6:30p STORM finish O/N STORM run of AbdA cells Cell culture changed media on 3 new Kc-cell flasks plated media on polyL coated coverglass. cells somewhat sparse, let’s give them some time to grow before fixing. Data clean-up: … Continue reading →

Posted in Summaries | Tagged , | Comments Off on Monday 08/26/13

Sunday 08/18/13

Posted on August 18, 2013 by admin

12:20p – 7:00p, 8:40p – 11:30p Goals reread and edit review analyze latest round of BXC data Probe making verify direction of MYcroArray BX-C Hox probes: probe region is “+” strand (antisense) T7 is on the nick side primer –> … Continue reading →

Posted in Summaries | Tagged , | Comments Off on Sunday 08/18/13

Saturday 08/17/13

Posted on August 17, 2013 by admin

10:30a – 10:30p Helping Hao align FRET Wrote SplitQVdax.m SplitDaxFRET_130817 Note: splitting large dax files is slow and memory intensive. Even 2000 frames takes a few gigs in the memory map approach. (10:30-2:30). Will need to help get setup with … Continue reading →

Posted in Summaries | Tagged , | Comments Off on Saturday 08/17/13

Friday 07/19/13

Posted on July 19, 2013 by admin

9:50 A – 5:30 P Banff finish draft schedule upload draft schedule to website finish activities sheet send participant email list, activities sheet, draft schedule, and notes about filming talks and requesting titles to Andrew. Planning with Jeff for next … Continue reading →

Posted in Summaries | Tagged , | Comments Off on Friday 07/19/13