Andrew:Notebook/AR150809 C1

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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

File:AR150809 hLINE.jpg

Size selection[edit]

File:AR150809 gels.jpg

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