Andrew:Notebook/AR150809 C1
Prep[edit]
Protocol[edit]
File:AR150809 reagents-page-001.jpg File:Protocol Worksheet AR150807 C1 v1-page-001.jpg File:Protocol Worksheet AR150807 C1 v1-page-002.jpg File:Protocol Worksheet AR150807 C1 v1-page-003.jpg File:AR150809 thermalProfile.png
Results[edit]
C1 capture[edit]
Chamber | Well | Number | LiveOrDead | Notes | After lysis |
Ch49 | A04 | 0 | dead | fragment | na |
Ch50 | A05 | 0 | dead | fragment | big_both |
Ch52 | A10 | 0 | dead | fragment | na |
Ch57 | B06 | 0 | na | na | na |
Ch59 | B11 | 0 | dead | fragment | na |
Ch63 | C06 | 0 | dead | fragment | na |
Ch21 | D01 | 0 | dead | fragment | na |
Ch67 | D04 | 0 | dead | fragment | na |
Ch72 | D12 | 0 | na | na | na |
Ch29 | E08 | 0 | na | na | na |
Ch77 | E11 | 0 | na | na | na |
Ch32 | F02 | 0 | dead | fragment | both_fragment_leftover |
Ch33 | F03 | 0 | dead | fragment | live_fragment_leftover |
Ch81 | F04 | 0 | dead | fragment | na |
Ch84 | F10 | 0 | na | na | na |
Ch82 | F12 | 0 | na | na | na |
Ch38 | G02 | 0 | dead | fragment | na |
Ch85 | G06 | 0 | dead | fragment | na |
Ch41 | G08 | 0 | dead | fragment | na |
Ch43 | H01 | 0 | na | na | na |
Ch93 | H04 | 0 | dead | fragment | na |
Ch92 | H05 | 0 | dead | fragment | na |
Ch46 | H07 | 0 | dead | fragment | na |
Ch95 | H11 | 0 | dead | fragment | na |
Ch94 | H12 | 0 | dead | fragment | na |
Ch03 | A01 | 1 | dead | weak_extravasating | na |
Ch02 | A02 | 1 | dead | fragment_weak | na |
Ch01 | A03 | 1 | dead | weak | na |
Ch51 | A06 | 1 | dead | weak | na |
Ch05 | A08 | 1 | dead | na | na |
Ch08 | B02 | 1 | dead | weak | na |
Ch55 | B04 | 1 | dead | na | na |
Ch56 | B05 | 1 | dead | extravasating_weak | na |
Ch11 | B08 | 1 | dead | big_bright | dead_fragment_leftover |
Ch58 | B10 | 1 | dead | na | na |
Ch17 | C08 | 1 | dead | big_bright | na |
Ch19 | D03 | 1 | dead | big_bright_bypass | na |
Ch78 | E10 | 1 | dead | bypass | na |
Ch76 | E12 | 1 | dead | bypass | na |
Ch31 | F01 | 1 | dead | bypass | both_fragment_leftover |
Ch35 | F08 | 1 | dead | na | na |
Ch45 | H03 | 1 | dead | extravasating_weak | na |
Ch47 | H08 | 1 | dead | fragment | na |
Ch96 | H10 | 1 | both | na | na |
Ch06 | A07 | 2 | dead | na | na |
Ch04 | A09 | 2 | dead | na | na |
Ch53 | A11 | 2 | dead | fragment | na |
Ch54 | A12 | 2 | dead | fragment | na |
Ch09 | B01 | 2 | dead | bypass | na |
Ch07 | B03 | 2 | dead | na | na |
Ch12 | B07 | 2 | dead | na | na |
Ch10 | B09 | 2 | dead | na | na |
Ch60 | B12 | 2 | dead | fragment | na |
Ch15 | C01 | 2 | dead | na | na |
Ch14 | C02 | 2 | dead | na | na |
Ch13 | C03 | 2 | dead | na | na |
Ch61 | C04 | 2 | dead | na | na |
Ch62 | C05 | 2 | dead | na | na |
Ch18 | C07 | 2 | dead | fragment_weak | na |
Ch16 | C09 | 2 | dead | na | na |
Ch64 | C10 | 2 | dead | fragment | na |
Ch65 | C11 | 2 | dead | fragment | na |
Ch66 | C12 | 2 | dead | fragment | na |
Ch20 | D02 | 2 | dead | fragment | na |
Ch68 | D05 | 2 | dead | fragment | na |
Ch69 | D06 | 2 | dead | fragment | na |
Ch24 | D07 | 2 | dead | small_fragment | na |
Ch23 | D08 | 2 | dead | na | na |
Ch22 | D09 | 2 | dead | na | na |
Ch70 | D10 | 2 | dead | na | na |
Ch71 | D11 | 2 | dead | fragment | na |
Ch25 | E01 | 2 | dead | small_fragment | na |
Ch26 | E02 | 2 | dead | small_fragment | na |
Ch27 | E03 | 2 | dead | small_fragment | na |
Ch75 | E04 | 2 | dead | fragment | na |
Ch74 | E05 | 2 | dead | na | na |
Ch73 | E06 | 2 | dead | fragment | na |
Ch28 | E07 | 2 | dead | small_fragment | both |
Ch30 | E09 | 2 | dead | small_fragment | na |
Ch80 | F05 | 2 | dead | fragment_bypass | na |
Ch79 | F06 | 2 | dead | fragment | na |
Ch34 | F07 | 2 | dead | na | na |
Ch36 | F09 | 2 | dead | fragment | na |
Ch83 | F11 | 2 | dead | fragment | na |
Ch37 | G01 | 2 | dead | na | na |
Ch39 | G03 | 2 | both | fragment | na |
Ch87 | G04 | 2 | both | fragment | na |
Ch86 | G05 | 2 | dead | na | na |
Ch40 | G07 | 2 | dead | fragment | na |
Ch42 | G09 | 2 | dead | fragment | na |
Ch90 | G10 | 2 | both | small_fragment | na |
Ch89 | G11 | 2 | dead | fragment | na |
Ch88 | G12 | 2 | dead | fragment | na |
Ch44 | H02 | 2 | dead | fragment | na |
Ch91 | H06 | 2 | dead | fragment | na |
Ch48 | H09 | 2 | both | na | na |
hLINE qPCR[edit]
qPCR was performed using hLINE primers on C1 MDA amplicons to quantify total yield
Size selection[edit]
Sequencing[edit]
C1 samples sequencing alongside GM12878 bulk in 150811_MiSeq
SampleID | Barcode |
AR-150809-Ch57ntc-B06-N701-S502 | TAAGGCGA-CTCTCTAT |
AR-150809-Ch72ntc-D12-N701-S503 | TAAGGCGA-CTCTCTAT |
AR-150809-Ch05-A08-N701-S504 | TAAGGCGA-CTCTCTAT |
AR-150809-Ch55-B04-N701-S505 | TAAGGCGA-CTCTCTAT |
AR-150809-Ch17-C08-N701-S506 | TAAGGCGA-CTCTCTAT |
AR-150809-Ch76-E12-N701-S507 | TAAGGCGA-CTCTCTAT |
AR-150809-Ch78-E10-N701-S508 | TAAGGCGA-CTCTCTAT |
AR-150809-Ch96-H10-N701-S517 | TAAGGCGA-CTCTCTAT |
AR-150809-Bulk-A-N702-S502 | TAAGGCGA-CTCTCTAT |
AR-150809-Bulk-B-N702-S503 | TAAGGCGA-CTCTCTAT |
AR-150809-Bulk-C-N702-S504 | TAAGGCGA-CTCTCTAT |
AR-150809-Bulk-D-N702-S505 | TAAGGCGA-CTCTCTAT |
AR-150809-Bulk-E-N702-S506 | TAAGGCGA-CTCTCTAT |
AR-150809-Bulk-F-N702-S507 | TAAGGCGA-CTCTCTAT |
AR-150809-Bulk-G-N702-S508 | TAAGGCGA-CTCTCTAT |
AR-150809-Bulk-H-N702-S517 | TAAGGCGA-CTCTCTAT |
CNV profiling[edit]
File:AR-150809-Ch05-A08-N701-S504.all.png File:AR-150809-Ch17-C08-N701-S506.all.png File:AR-150809-Ch55-B04-N701-S505.all.png File:AR-150809-Ch57ntc-B06-N701-S502.all.png File:AR-150809-Ch72ntc-D12-N701-S503.all.png File:AR-150809-Ch76-E12-N701-S507.all.png File:AR-150809-Ch78-E10-N701-S508.all.png File:AR-150809-Ch96-H10-N701-S517.all.png
MAPD profiling[edit]
File:AR-150809-Ch05-A08-N701-S504 mapd.png File:AR-150809-Ch17-C08-N701-S506 mapd.png File:AR-150809-Ch55-B04-N701-S505 mapd.png File:AR-150809-Ch57ntc-B06-N701-S502 mapd.png File:AR-150809-Ch72ntc-D12-N701-S503 mapd.png File:AR-150809-Ch76-E12-N701-S507 mapd.png File:AR-150809-Ch78-E10-N701-S508 mapd.png File:AR-150809-Ch96-H10-N701-S517 mapd.png