Andrew:Notebook/AR150720 C1

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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]

File:AR150720 C1Slide1.png

File:AR150720 C1Slide2.png

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

MAPD[edit]

File:AR150720 mapd Slide1.jpg

File:AR150720 mapd Slide2.jpg