Arichard:Notebook/midas140917

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MIDAS run from September 17, 2014[edit]

Sample tracking[edit]

Sample # Sample description Array Image pos. Index # Barcode
1 NeuN+ Cbl 7-03 sorted May 20 1 1 1 ATCACG
2 NeuN+ Cbl 7-03 sorted May 21 1 2 2 CGATGT
3 NeuN+ Cbl 7-03 sorted May 22 2 3 4 TGACCA
4 NeuN+ Cbl 7-03 sorted May 23 2 5 5 ACAGTG
5 NeuN+ Cbl 7-03 sorted May 24 3 6 6 GCCAAT
6 NeuN+ Cbl 7-03 sorted May 25 3 7 7 CAGATC
7 NeuN+ Cbl 7-03 sorted May 26 3 7 10 TAGCTT
8 NeuN+ Cbl 7-03 sorted May 27 4 8 8 ACTTGA
9 NTC from loaded array 4 8 11 GGCTAC
10 NeuN+ Cbl 25-00 sorted May 27 5 10 12 CTTGTA
11 NeuN+ Cbl 25-00 sorted May 28 5 10 13 CCATGA
12 NeuN+ Cbl 25-00 sorted May 29 5 11 14 AAGACA
13 NeuN+ Cbl 25-00 sorted May 30 5 11 15 CTTCCT
14 NeuN+ Cbl 25-00 sorted May 31 6 12 25 TACTGC
15 NeuN+ Cbl 25-00 sorted May 32 6 12 26 TCGTGA
16 NeuN+ Cbl 25-00 sorted May 33 6 13 16 GGGGTT
17 NeuN+ Cbl 25-00 sorted May 34 6 13 27 TACGCG
18 NeuN+ Cbl 25-00 sorted May 35 7 14 28 AGGTGC
19 NeuN+ Cbl 25-00 sorted May 36 7 14 29 ACGAAC
20 NeuN+ Cbl 25-00 sorted May 37 7 15 30 TTAGTG
21 NeuN+ Cbl 25-00 sorted May 38 8 16 31 CACCAC
22 NeuN+ Cbl 25-00 sorted May 39 8 16 33 CGCAAC
23 NeuN+ Cbl 25-00 sorted May 40 8 17 34 AACTGA
24 NTC from loaded array 8 17 35 ATCGGG
  • I used a different type of array, the last one from the Groisman lab.
  • It contained a type of bulk blocking treatment that would wet and block PDMS pores without BSA.
  • They told me to use it without BSA, but I used BSA anyways.
  • I saw a lot of wrinkling in the bottom of the array due to its thinness. This created a lot of issues with imaging and picking.

Gels[edit]

File:Midas140917GelsSlide1.jpg File:Midas140917GelsSlide2.jpg File:Midas140917GelsSlide3.jpg File:Midas140917GelsSlide4.jpg File:Midas140917GelsSlide5.jpg File:Midas140917GelsSlide6.jpg

Sequencing[edit]

ID Index Sequence # of Reads Run Type, Minmum BP Library Size Gel Image Read 1 Sequencing Primer Index Primer Read 2 Sequencing Primer
INITIAL-PROJECT-SAMPLE-DATE-Index CGTGCA Million SE/PE, 36+6+36 SIZE RANGE (BP) Link Name Name Name
AR65-PL703May20-Sep17-7 CAGATC 20 SE 50+7 200-800 http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140917 Nextera_R1 Nextera_Ind NA
AR66-PL703May20-Sep17-8 ACTTGA 20 SE 50+7 200-800 http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140917 Nextera_R1 Nextera_Ind NA
AR67-PL703May20-Sep17-12 CTTGTA 20 SE 50+7 200-800 http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140917 Nextera_R1 Nextera_Ind NA
AR68-PL2500May20-Sep17-25 TACTGC 20 SE 50+7 200-800 http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140917 Nextera_R1 Nextera_Ind NA
AR69-PL2500May20-Sep17-26 TCGTGA 20 SE 50+7 200-800 http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140917 Nextera_R1 Nextera_Ind NA
AR70-PL2500May20-Sep17-16 GGGGTT 20 SE 50+7 200-800 http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140917 Nextera_R1 Nextera_Ind NA
AR71-PL2500May20-Sep17-34 AACTGA 20 SE 50+7 200-800 http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140917 Nextera_R1 Nextera_Ind NA
AR72-PL2500May20NTC-Sep17-35 ATCGGG 20 SE 50+7 200-800 http://genome-tech.ucsd.edu/LabNotes/index.php/Arichard:Notebook/midas140917 Nextera_R1 Nextera_Ind NA