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==Planning== ===Motivation=== 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=== [[File:AR150720_reagents-page-001.jpg|600px]] [[File:Protocol Worksheet AR150720_C1 v1-page-001.jpg|600px]] [[File:Protocol Worksheet AR150720_C1 v1-page-002.jpg|600px]] [[File:Protocol Worksheet AR150720_C1 v1-page-003.jpg|600px]] [[File:AR150720_thermalProfile.png|600px]] ==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;"|'''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=== [[File:AR150720_C1Slide1.png | 600px]] [[File:AR150720_C1Slide2.png | 600px]] ===Sequencing=== {| {{table}} | align="center" style="background:#f0f0f0;"|'''AR-150720-Ch05-A08-N702-S517''' | align="center" style="background:#f0f0f0;"|'''CGTACTAG-GCGTAAGA''' | align="center" style="background:#f0f0f0;"|'''4''' | align="center" style="background:#f0f0f0;"|'''SE50+8+8''' | align="center" style="background:#f0f0f0;"|'''200-800''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''HP10''' | align="center" style="background:#f0f0f0;"|'''HP12''' | align="center" style="background:#f0f0f0;"|'''NA''' | align="center" style="background:#f0f0f0;"|'''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 |- | |} {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Index Sequence''' | align="center" style="background:#f0f0f0;"|'''# of Reads''' | align="center" style="background:#f0f0f0;"|'''Run Type, Minmum BP''' | align="center" style="background:#f0f0f0;"|'''Library Size''' | align="center" style="background:#f0f0f0;"|'''Gel Image''' | align="center" style="background:#f0f0f0;"|'''Read 1 Sequencing Primer''' | align="center" style="background:#f0f0f0;"|'''Index Primer''' | align="center" style="background:#f0f0f0;"|'''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=== [[File:AR-150720-Ch05-A08-N702-S517.all.png|600px]] [[File:AR-150720-Ch12-B07-N703-S502.all.png|600px]] [[File:AR-150720-Ch13-C03-N704-S503.all.png|600px]] [[File:AR-150720-Ch24-D07-N702-S503.all.png|600px]] [[File:AR-150720-Ch28-E07-N703-S503.all.png|600px]] [[File:AR-150720-Ch30-E09-N705-S503.all.png|600px]] [[File:AR-150720-Ch34-F07-N702-S504.all.png|600px]] [[File:AR-150720-Ch37-G01-N703-S504.all.png|600px]] [[File:AR-150720-Ch38-G02-N704-S504.all.png|600px]] [[File:AR-150720-Ch45-H03-N705-S504.all.png|600px]] [[File:AR-150720-Ch90-G10-N705-S504.all.png|600px]] ===MAPD=== [[File:AR150720_mapd_Slide1.jpg|600px]] [[File:AR150720_mapd_Slide2.jpg|600px]]
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