Arichard:Notebook/midas140911
Jump to navigation
Jump to search
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
Gel lane | Sample type | Array#Pos# | Index | 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
File:Midas140911GelsSlide2.jpg
File:Midas140911GelsSlide3.jpg
File:Midas140911GelsSlide4.jpg
File:Midas140911GelsSlide5.jpg
File:Midas140911GelsSlide6.jpg
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
- 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?
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.