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==MIDAS, September 11, 2014 (midas140911)== * Gwen asked for a run with only cerebellum, all of which is NeuN +, with both AD patient 25-00 and control patient 7-03 in the same run. * Based on positive results from the last run (midas140828), I removed the buffer headspace from all microwell arrays before adding oil overlay. This was an effort to prevent runaway reactions. * Also based on positive results from the last run, I skipped ALS/NS/PolI and EtOH precipitation before Nextera. This made the run much faster. ===Samples=== {| {{table}} | align="center" style="background:#f0f0f0;"|'''Gel lane''' | align="center" style="background:#f0f0f0;"|'''Sample type''' | align="center" style="background:#f0f0f0;"|'''Array#Pos#''' | align="center" style="background:#f0f0f0;"|'''Index''' | align="center" style="background:#f0f0f0;"|'''SeqID (If selected)''' |- | 1||NeuN+ Cbl from 7-03 sorted May 20, 2014||a1p1||16||AR56-PL703May20-Sep11-16 |- | 2||NeuN+ Cbl from 7-03 sorted May 20, 2014||a1p1||25||AR57-PL703May20-Sep11-25 |- | 3||NeuN+ Cbl from 7-03 sorted May 20, 2014||a2p3||26||N/A |- | 4||NeuN+ Cbl from 7-03 sorted May 20, 2014||a2p3||27||N/A |- | 5||NeuN+ Cbl from 7-03 sorted May 20, 2014||a2p4||28||AR58-PL703May20-Sep11-28 |- | 6||NeuN+ Cbl from 7-03 sorted May 20, 2014||a3p7||29||AR59-PL703May20-Sep11-29 |- | 7||NeuN+ Cbl from 7-03 sorted May 20, 2014||a3p9||30||N/A |- | 8||NeuN+ Cbl from 7-03 sorted May 20, 2014||a3p10||31||AR60-PL703May20-Sep11-31 |- | 9||NeuN+ Cbl from 7-03 sorted May 20, 2014||a4p11||33||N/A |- | 10||NeuN+ Cbl from 7-03 sorted May 20, 2014||a4p12||34||N/A |- | 11||NeuN+ Cbl from 7-03 sorted May 20, 2014||a4p12||35||N/A |- | 12||NTC from+B51 array loaded with 7-03||a4p12ntc||36||N/A |- | 13||NeuN+ Cbl from 25-00 sorted May 20, 2014||a5p13||37||AR61-PL2500May20-Sep11-37 |- | 14||NeuN+ Cbl from 25-00 sorted May 20, 2014||a5p13||38||AR62-PL2500May20-Sep11-38 |- | 15||NeuN+ Cbl from 25-00 sorted May 20, 2014||a6p14||39||N/A |- | 16||NeuN+ Cbl from 25-00 sorted May 20, 2014||a6p14||40||N/A |- | 17||NeuN+ Cbl from 25-00 sorted May 20, 2014||a6p15||41||N/A |- | 18||NeuN+ Cbl from 25-00 sorted May 20, 2014||a7p17||42||AR63-PL2500May20-Sep11-42 |- | 19||NeuN+ Cbl from 25-00 sorted May 20, 2014||a7p18||43||AR64-PL2500May20-Sep11-43 |- | 20||NeuN+ Cbl from 25-00 sorted May 20, 2014||a8p20||44||N/A |- | 21||NeuN+ Cbl from 25-00 sorted May 20, 2014||a8p20||45||N/A |- | 22||NeuN+ Cbl from 25-00 sorted May 20, 2014||a8p21||46||N/A |- | 23||NeuN+ Cbl from 25-00 sorted May 20, 2014||a8p22||47||N/A |- | 24||NTC from array loaded with 25-00||a8p21ntc||48||N/A |- | |} ===Size select gels after Nextera=== [[File:midas140911GelsSlide1.jpg|400px]] [[File:midas140911GelsSlide2.jpg|400px]] [[File:midas140911GelsSlide3.jpg|400px]] [[File:midas140911GelsSlide4.jpg|400px]] [[File:midas140911GelsSlide5.jpg|400px]] [[File:midas140911GelsSlide6.jpg|400px]] ===Sequencing=== * These libraries were submitted for sequencing in HL173. They were not screened. ==MagVigen DNA Select Focus 300/600 beads== Motivation * PA gel size selection is time and labor intensive. NVigen makes a kit called MagVigen DNA select 300/600 (Cat #Kr61001-300/600) for NGS library prep. This would save ~0.5 to 1 day on each run. Goal * Answer each of the following questions: ** What is the loading capacity of the beads? ** How clean is the selection? ** Will the library cluster as densely? ** Will the pass filter rate suffer? * Run side-by-side gel comparison of bead vs. PA gel size selection and send the gel images to Aihua at NVigen as per our agreement. Strategy * Save 5 out of 20 ul from each of 9 libraries (only high-concentration libraries as assessed by PA gel) to pool and run on MagVigen beads. I carried on with size selection for the remaining 15 ul of each of the 9 positive libraries. ===Samples=== ===Gel result=== [[File:.jpg|400px]] ===Sequencing===
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