Andrew:Notebook/AR150809 C1: Difference between revisions

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==Results==
==Results==
===C1 capture===
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Chamber'''
| align="center" style="background:#f0f0f0;"|'''Well'''
| align="center" style="background:#f0f0f0;"|'''Number'''
| align="center" style="background:#f0f0f0;"|'''LiveOrDead'''
| align="center" style="background:#f0f0f0;"|'''Notes'''
| align="center" style="background:#f0f0f0;"|'''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===
qPCR was performed using hLINE primers on C1 MDA amplicons to quantify total yield
[[File:AR150809_hLINE.jpg|600px]]
===Size selection===
[[File:AR150809_gels.jpg|600px]]
===Sequencing===
C1 samples sequencing alongside GM12878 bulk in 150811_MiSeq
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''SampleID'''
| align="center" style="background:#f0f0f0;"|'''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===
[[File:AR-150809-Ch05-A08-N701-S504.all.png|600px]]
[[File:AR-150809-Ch17-C08-N701-S506.all.png|600px]]
[[File:AR-150809-Ch55-B04-N701-S505.all.png|600px]]
[[File:AR-150809-Ch57ntc-B06-N701-S502.all.png|600px]]
[[File:AR-150809-Ch72ntc-D12-N701-S503.all.png|600px]]
[[File:AR-150809-Ch76-E12-N701-S507.all.png|600px]]
[[File:AR-150809-Ch78-E10-N701-S508.all.png|600px]]
[[File:AR-150809-Ch96-H10-N701-S517.all.png|600px]]
===MAPD profiling===
[[File:AR-150809-Ch05-A08-N701-S504_mapd.png|600px]]
[[File:AR-150809-Ch17-C08-N701-S506_mapd.png|600px]]
[[File:AR-150809-Ch55-B04-N701-S505_mapd.png|600px]]
[[File:AR-150809-Ch57ntc-B06-N701-S502_mapd.png|600px]]
[[File:AR-150809-Ch72ntc-D12-N701-S503_mapd.png|600px]]
[[File:AR-150809-Ch76-E12-N701-S507_mapd.png|600px]]
[[File:AR-150809-Ch78-E10-N701-S508_mapd.png|600px]]
[[File:AR-150809-Ch96-H10-N701-S517_mapd.png|600px]]

Latest revision as of 22:32, 14 September 2015

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