Andrew:Notebook/AR150720 C1
Planning[edit]
Motivation[edit]
Based on the relative success of the previous sequential MDA experiment, we decided to repeat with an unmodified primer (N9) in the first step. The concept is that Phi29 will digest excess primer in order to minimize exponential gain.
Protocol[edit]
File:AR150720 reagents-page-001.jpg
File:Protocol Worksheet AR150720 C1 v1-page-001.jpg
File:Protocol Worksheet AR150720 C1 v1-page-002.jpg
File:Protocol Worksheet AR150720 C1 v1-page-003.jpg
File:AR150720 thermalProfile.png
Results[edit]
C1 capture[edit]
Chamber | Well | Number | LiveOrDead | Notes | Library prep |
Ch01 | A03 | empty | na | na | |
Ch02 | A02 | empty | na | na | |
Ch03 | A01 | empty | na | na | |
Ch04 | A09 | empty | na | na | |
Ch05 | A08 | single | dead | na | |
Ch06 | A07 | multiple | na | na | |
Ch07 | B03 | empty | na | botched image | |
Ch08 | B02 | empty | na | na | |
Ch09 | B01 | single | dead | weak | |
Ch10 | B09 | single | dead | fragment/weak | |
Ch11 | B08 | empty | na | na | |
Ch12 | B07 | single | dead | na | |
Ch13 | C03 | single | dead | na | |
Ch14 | C02 | empty | na | na | |
Ch15 | C01 | empty | na | na | |
Ch16 | C09 | empty | dead | fragment/weak | |
Ch17 | C08 | multiple | na | na | |
Ch18 | C07 | multiple | dead | na | |
Ch19 | D03 | single | dead | na | |
Ch20 | D02 | single | dead | na | |
Ch21 | D01 | multiple | na | na | |
Ch22 | D09 | single | dead | fragment/weak | |
Ch23 | Ch | single | dead | na | |
Ch24 | D07 | single | dead | na | 7/27/2015 |
Ch25 | E01 | empty | na | na | |
Ch26 | E02 | empty | na | na | |
Ch27 | E03 | multiple | na | na | |
Ch28 | E07 | single | dead | na | 7/27/2015 |
Ch29 | E08 | single | dead | na | 7/27/2015 |
Ch30 | E09 | single | dead | na | 7/27/2015 |
Ch31 | F01 | single | dead | na | |
Ch32 | F02 | single | dead | na | |
Ch33 | F03 | single | dead | fragment/weak | |
Ch34 | F07 | single | dead | na | 7/27/2015 |
Ch35 | F08 | single | dead | na | |
Ch36 | F09 | multiple | na | na | |
Ch37 | G01 | single | dead | na | 7/27/2015 |
Ch38 | G02 | single | dead | na | 7/27/2015 |
Ch39 | G03 | single | dead | na | |
Ch40 | G07 | single | dead | na | |
Ch41 | G08 | multiple | na | na | |
Ch42 | G09 | empty | na | na | |
Ch43 | H01 | single | dead | na | |
Ch44 | H02 | single | dead | na | |
Ch45 | H03 | single | live | extravasating | |
Ch46 | H07 | single | dead | extravasating | |
Ch47 | H08 | multiple | na | na | |
Ch48 | H09 | single | both | extravasating | |
Ch49 | A04 | empty | na | na | |
Ch50 | A05 | single | dead | fragment | |
Ch51 | A06 | empty | na | na | |
Ch52 | A10 | single | dead | extravasating | |
Ch53 | A11 | empty | na | na | |
Ch54 | A12 | single | dead | extravasating | |
Ch55 | B04 | single | dead | na | |
Ch56 | B05 | empty | na | na | |
Ch57 | B06 | empty | na | na | |
Ch58 | B10 | empty | na | na | |
Ch59 | B11 | empty | na | na | |
Ch60 | B12 | single | dead | weak | |
Ch61 | C04 | single | dead | fragment/weak | |
Ch62 | C05 | empty | dead | fragment | |
Ch63 | C06 | single | dead | na | |
Ch64 | C10 | single | dead | extravasating | |
Ch65 | C11 | empty | na | debris | |
Ch66 | C12 | single | dead | na | |
Ch67 | D04 | empty | na | na | |
Ch68 | D05 | single | dead | fragment/weak | |
Ch69 | D06 | empty | na | na | |
Ch70 | D10 | single | dead | fragment | |
Ch71 | D11 | single | dead | na | |
Ch72 | D12 | multiple | na | na | |
Ch73 | E06 | single | dead | debris | |
Ch74 | E05 | empty | na | na | |
Ch75 | E04 | empty | na | na | |
Ch76 | E12 | empty | na | debris | |
Ch77 | E11 | single | dead | extravasating | |
Ch78 | E10 | single | dead | weak | |
Ch79 | F06 | single | dead | fragment/weak | |
Ch80 | F05 | single | dead | na | |
Ch81 | F04 | empty | na | na | |
Ch82 | F12 | single | dead | weak | |
Ch83 | F11 | empty | na | na | |
Ch84 | F10 | single | dead | weak | |
Ch85 | G06 | multiple | na | na | |
Ch86 | G05 | multiple | na | na | |
Ch87 | G04 | single | dead | na | |
Ch88 | G12 | multiple | na | na | |
Ch89 | G11 | single | dead | weak | |
Ch90 | G10 | single | live | extravasating/weak | 7/27/2015 |
Ch91 | H06 | single | dead | na | |
Ch92 | H05 | multiple | na | na | |
Ch93 | H04 | multiple | na | na | |
Ch94 | H12 | single | dead | weak | |
Ch95 | H11 | single | dead | na | |
Ch96 | H10 | multiple | na | na | |
Size selection[edit]
Sequencing[edit]
AR-150720-Ch05-A08-N702-S517 | CGTACTAG-GCGTAAGA | 4 | SE50+8+8 | 200-800 | ' | HP10 | HP12 | NA | Tube labeled AR-150720-Ch05 |
AR-150720-Ch12-B07-N703-S502 | AGGCAGAA-CTCTCTAT | 4 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | Tube labeled AR-150720-Ch12 | |
AR-150720-Ch13-C03-N704-S503 | TCCTGAGC-TATCCTCT | 4 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | Tube labeled AR-150720-Ch13 | |
AR-150720-Ch45-H03-N705-S504 | GGACTCCT-AGAGTAGA | 4 | SE50+8+8 | 200-800 | HP10 | HP12 | NA | Tube labeled AR-150720-Ch45 | |
Sample 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 |
AR-150720-Ch24-D07-N702-S503 | CGTACTAG-TATCCTCT | 2 | SE50+8+8 | 200-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/Andrew:Notebook/AR150720_C1 | HP10 | HP12 | NA |
AR-150720-Ch28-E07-N703-S503 | AGGCAGAA-TATCCTCT | 2 | SE50+8+8 | 200-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/Andrew:Notebook/AR150720_C1 | HP10 | HP12 | NA |
AR-150720-Ch29-E08-N704-S503 | TCCTGAGC-TATCCTCT | 2 | SE50+8+8 | 200-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/Andrew:Notebook/AR150720_C1 | HP10 | HP12 | NA |
AR-150720-Ch30-E09-N705-S503 | GGACTCCT-TATCCTCT | 2 | SE50+8+8 | 200-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/Andrew:Notebook/AR150720_C1 | HP10 | HP12 | NA |
AR-150720-Ch34-F07-N702-S504 | CGTACTAG-AGAGTAGA | 2 | SE50+8+8 | 200-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/Andrew:Notebook/AR150720_C1 | HP10 | HP12 | NA |
AR-150720-Ch37-G01-N703-S504 | AGGCAGAA-AGAGTAGA | 2 | SE50+8+8 | 200-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/Andrew:Notebook/AR150720_C1 | HP10 | HP12 | NA |
AR-150720-Ch38-G02-N704-S504 | TCCTGAGC-AGAGTAGA | 2 | SE50+8+8 | 200-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/Andrew:Notebook/AR150720_C1 | HP10 | HP12 | NA |
AR-150720-Ch90-G10-N705-S504 | GGACTCCT-AGAGTAGA | 2 | SE50+8+8 | 200-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/Andrew:Notebook/AR150720_C1 | HP10 | HP12 | NA |
CNV profiling[edit]
File:AR-150720-Ch05-A08-N702-S517.all.png File:AR-150720-Ch12-B07-N703-S502.all.png File:AR-150720-Ch13-C03-N704-S503.all.png File:AR-150720-Ch24-D07-N702-S503.all.png File:AR-150720-Ch28-E07-N703-S503.all.png File:AR-150720-Ch30-E09-N705-S503.all.png File:AR-150720-Ch34-F07-N702-S504.all.png File:AR-150720-Ch37-G01-N703-S504.all.png File:AR-150720-Ch38-G02-N704-S504.all.png File:AR-150720-Ch45-H03-N705-S504.all.png File:AR-150720-Ch90-G10-N705-S504.all.png