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
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