Andrew:Notebook/AR150618 C1: Difference between revisions
>Andrew (Created page with "==31 nL MDA on C1 with GM12878== ===Overview=== ====Motivation==== ====Goal==== ===Protocol=== ====Reagents==== ===Results=== ====qPCR==== ====Gels==== [File:AR150618...") |
>Andrew |
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====Motivation==== | ====Motivation==== | ||
[[File:AR150618_motivation.png|1500px]] | |||
===Protocol=== | ====Reagents==== | ||
[[File:AR150618_reagents.jpg|800px]] | |||
====Protocol==== | |||
[[File:Protocol Worksheet AR150618_C1 v1-1.png|800px]] | |||
[[File:Protocol Worksheet AR150618_C1 v1-2.png|800px]] | |||
[[File:Protocol Worksheet AR150618_C1 v1-3.png|800px]] | |||
[[File:AR150618_thermalProfile.png|800px]] | |||
===Results=== | ===Results=== | ||
==== | ====Cell capture==== | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Initials''' | |||
| align="center" style="background:#f0f0f0;"|'''Date (YYMMDD)''' | |||
| align="center" style="background:#f0f0f0;"|'''Chamber''' | |||
| align="center" style="background:#f0f0f0;"|'''Well''' | |||
| align="center" style="background:#f0f0f0;"|'''i7''' | |||
| align="center" style="background:#f0f0f0;"|'''i5''' | |||
| align="center" style="background:#f0f0f0;"|'''i7 sequence (RC)''' | |||
| align="center" style="background:#f0f0f0;"|'''i5 barcode''' | |||
| align="center" style="background:#f0f0f0;"|'''SampleID''' | |||
| align="center" style="background:#f0f0f0;"|'''Full barcode''' | |||
| align="center" style="background:#f0f0f0;"|'''Number''' | |||
| align="center" style="background:#f0f0f0;"|'''LiveOrDead''' | |||
| align="center" style="background:#f0f0f0;"|'''Notes''' | |||
|- | |||
| AR||150618||Ch03||A01||N701||S502||TAAGGCGA||CTCTCTAT||AR-150618-Ch03-A01-N701-S502||TAAGGCGA-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch02||A02||N702||S502||CGTACTAG||CTCTCTAT||AR-150618-Ch02-A02-N702-S502||CGTACTAG-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch01||A03||N703||S502||AGGCAGAA||CTCTCTAT||AR-150618-Ch01-A03-N703-S502||AGGCAGAA-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch49||A04||N704||S502||TCCTGAGC||CTCTCTAT||AR-150618-Ch49-A04-N704-S502||TCCTGAGC-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch50||A05||N705||S502||GGACTCCT||CTCTCTAT||AR-150618-Ch50-A05-N705-S502||GGACTCCT-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch51||A06||N706||S502||TAGGCATG||CTCTCTAT||AR-150618-Ch51-A06-N706-S502||TAGGCATG-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch06||A07||N707||S502||CTCTCTAC||CTCTCTAT||AR-150618-Ch06-A07-N707-S502||CTCTCTAC-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch05||A08||N710||S502||CGAGGCTG||CTCTCTAT||AR-150618-Ch05-A08-N710-S502||CGAGGCTG-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch04||A09||N711||S502||AAGAGGCA||CTCTCTAT||AR-150618-Ch04-A09-N711-S502||AAGAGGCA-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch52||A10||N712||S502||GTAGAGGA||CTCTCTAT||AR-150618-Ch52-A10-N712-S502||GTAGAGGA-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch53||A11||N714||S502||GCTCATGA||CTCTCTAT||AR-150618-Ch53-A11-N714-S502||GCTCATGA-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch54||A12||N715||S502||ATCTCAGG||CTCTCTAT||AR-150618-Ch54-A12-N715-S502||ATCTCAGG-CTCTCTAT||0||na||na | |||
|- | |||
| AR||150618||Ch09||B01||N701||S503||TAAGGCGA||TATCCTCT||AR-150618-Ch09-B01-N701-S503||TAAGGCGA-TATCCTCT||0||na||na | |||
|- | |||
| AR||150618||Ch08||B02||N702||S503||CGTACTAG||TATCCTCT||AR-150618-Ch08-B02-N702-S503||CGTACTAG-TATCCTCT||0||na||na | |||
|- | |||
| AR||150618||Ch07||B03||N703||S503||AGGCAGAA||TATCCTCT||AR-150618-Ch07-B03-N703-S503||AGGCAGAA-TATCCTCT||1||dead||na | |||
|- | |||
| AR||150618||Ch55||B04||N704||S503||TCCTGAGC||TATCCTCT||AR-150618-Ch55-B04-N704-S503||TCCTGAGC-TATCCTCT||0||na||na | |||
|- | |||
| AR||150618||Ch56||B05||N705||S503||GGACTCCT||TATCCTCT||AR-150618-Ch56-B05-N705-S503||GGACTCCT-TATCCTCT||0||na||na | |||
|- | |||
| AR||150618||Ch57||B06||N706||S503||TAGGCATG||TATCCTCT||AR-150618-Ch57-B06-N706-S503||TAGGCATG-TATCCTCT||0||na||na | |||
|- | |||
| AR||150618||Ch12||B07||N707||S503||CTCTCTAC||TATCCTCT||AR-150618-Ch12-B07-N707-S503||CTCTCTAC-TATCCTCT||1||dead||na | |||
|- | |||
| AR||150618||Ch11||B08||N710||S503||CGAGGCTG||TATCCTCT||AR-150618-Ch11-B08-N710-S503||CGAGGCTG-TATCCTCT||3||dead||na | |||
|- | |||
| AR||150618||Ch10||B09||N711||S503||AAGAGGCA||TATCCTCT||AR-150618-Ch10-B09-N711-S503||AAGAGGCA-TATCCTCT||1||dead||weak | |||
|- | |||
| AR||150618||Ch58||B10||N712||S503||GTAGAGGA||TATCCTCT||AR-150618-Ch58-B10-N712-S503||GTAGAGGA-TATCCTCT||0||na||na | |||
|- | |||
| AR||150618||Ch59||B11||N714||S503||GCTCATGA||TATCCTCT||AR-150618-Ch59-B11-N714-S503||GCTCATGA-TATCCTCT||0||na||na | |||
|- | |||
| AR||150618||Ch60||B12||N715||S503||ATCTCAGG||TATCCTCT||AR-150618-Ch60-B12-N715-S503||ATCTCAGG-TATCCTCT||0||na||na | |||
|- | |||
| AR||150618||Ch15||C01||N701||S505||TAAGGCGA||GTAAGGAG||AR-150618-Ch15-C01-N701-S505||TAAGGCGA-GTAAGGAG||2||dead||na | |||
|- | |||
| AR||150618||Ch14||C02||N702||S505||CGTACTAG||GTAAGGAG||AR-150618-Ch14-C02-N702-S505||CGTACTAG-GTAAGGAG||1||dead||lumpy | |||
|- | |||
| AR||150618||Ch13||C03||N703||S505||AGGCAGAA||GTAAGGAG||AR-150618-Ch13-C03-N703-S505||AGGCAGAA-GTAAGGAG||1||live||extravasating | |||
|- | |||
| AR||150618||Ch61||C04||N704||S505||TCCTGAGC||GTAAGGAG||AR-150618-Ch61-C04-N704-S505||TCCTGAGC-GTAAGGAG||1||dead||weak | |||
|- | |||
| AR||150618||Ch62||C05||N705||S505||GGACTCCT||GTAAGGAG||AR-150618-Ch62-C05-N705-S505||GGACTCCT-GTAAGGAG||0||na||na | |||
|- | |||
| AR||150618||Ch63||C06||N706||S505||TAGGCATG||GTAAGGAG||AR-150618-Ch63-C06-N706-S505||TAGGCATG-GTAAGGAG||0||na||na | |||
|- | |||
| AR||150618||Ch18||C07||N707||S505||CTCTCTAC||GTAAGGAG||AR-150618-Ch18-C07-N707-S505||CTCTCTAC-GTAAGGAG||1||both||extravasating | |||
|- | |||
| AR||150618||Ch17||C08||N710||S505||CGAGGCTG||GTAAGGAG||AR-150618-Ch17-C08-N710-S505||CGAGGCTG-GTAAGGAG||1||live||extravasating | |||
|- | |||
| AR||150618||Ch16||C09||N711||S505||AAGAGGCA||GTAAGGAG||AR-150618-Ch16-C09-N711-S505||AAGAGGCA-GTAAGGAG||1||both||na | |||
|- | |||
| AR||150618||Ch64||C10||N712||S505||GTAGAGGA||GTAAGGAG||AR-150618-Ch64-C10-N712-S505||GTAGAGGA-GTAAGGAG||0||na||na | |||
|- | |||
| AR||150618||Ch65||C11||N714||S505||GCTCATGA||GTAAGGAG||AR-150618-Ch65-C11-N714-S505||GCTCATGA-GTAAGGAG||0||na||na | |||
|- | |||
| AR||150618||Ch66||C12||N715||S505||ATCTCAGG||GTAAGGAG||AR-150618-Ch66-C12-N715-S505||ATCTCAGG-GTAAGGAG||0||na||na | |||
|- | |||
| AR||150618||Ch21||D01||N701||S506||TAAGGCGA||ACTGCATA||AR-150618-Ch21-D01-N701-S506||TAAGGCGA-ACTGCATA||1||live||extravasating | |||
|- | |||
| AR||150618||Ch20||D02||N702||S506||CGTACTAG||ACTGCATA||AR-150618-Ch20-D02-N702-S506||CGTACTAG-ACTGCATA||1||dead||na | |||
|- | |||
| AR||150618||Ch19||D03||N703||S506||AGGCAGAA||ACTGCATA||AR-150618-Ch19-D03-N703-S506||AGGCAGAA-ACTGCATA||0||na||na | |||
|- | |||
| AR||150618||Ch67||D04||N704||S506||TCCTGAGC||ACTGCATA||AR-150618-Ch67-D04-N704-S506||TCCTGAGC-ACTGCATA||0||na||na | |||
|- | |||
| AR||150618||Ch68||D05||N705||S506||GGACTCCT||ACTGCATA||AR-150618-Ch68-D05-N705-S506||GGACTCCT-ACTGCATA||0||na||na | |||
|- | |||
| AR||150618||Ch69||D06||N706||S506||TAGGCATG||ACTGCATA||AR-150618-Ch69-D06-N706-S506||TAGGCATG-ACTGCATA||0||na||na | |||
|- | |||
| AR||150618||Ch24||D07||N707||S506||CTCTCTAC||ACTGCATA||AR-150618-Ch24-D07-N707-S506||CTCTCTAC-ACTGCATA||1||dead||extravasating | |||
|- | |||
| AR||150618||Ch23||D08||N710||S506||CGAGGCTG||ACTGCATA||AR-150618-Ch23-D08-N710-S506||CGAGGCTG-ACTGCATA||1||dead||na | |||
|- | |||
| AR||150618||Ch22||D09||N711||S506||AAGAGGCA||ACTGCATA||AR-150618-Ch22-D09-N711-S506||AAGAGGCA-ACTGCATA||1||live||extravasating | |||
|- | |||
| AR||150618||Ch70||D10||N712||S506||GTAGAGGA||ACTGCATA||AR-150618-Ch70-D10-N712-S506||GTAGAGGA-ACTGCATA||1||dead||extravasating | |||
|- | |||
| AR||150618||Ch71||D11||N714||S506||GCTCATGA||ACTGCATA||AR-150618-Ch71-D11-N714-S506||GCTCATGA-ACTGCATA||0||na||na | |||
|- | |||
| AR||150618||Ch72||D12||N715||S506||ATCTCAGG||ACTGCATA||AR-150618-Ch72-D12-N715-S506||ATCTCAGG-ACTGCATA||0||na||na | |||
|- | |||
| AR||150618||Ch25||E01||N701||S507||TAAGGCGA||AAGGAGTA||AR-150618-Ch25-E01-N701-S507||TAAGGCGA-AAGGAGTA||1||live||weak | |||
|- | |||
| AR||150618||Ch26||E02||N702||S507||CGTACTAG||AAGGAGTA||AR-150618-Ch26-E02-N702-S507||CGTACTAG-AAGGAGTA||0||na||na | |||
|- | |||
| AR||150618||Ch27||E03||N703||S507||AGGCAGAA||AAGGAGTA||AR-150618-Ch27-E03-N703-S507||AGGCAGAA-AAGGAGTA||0||na||na | |||
|- | |||
| AR||150618||Ch75||E04||N704||S507||TCCTGAGC||AAGGAGTA||AR-150618-Ch75-E04-N704-S507||TCCTGAGC-AAGGAGTA||0||na||na | |||
|- | |||
| AR||150618||Ch74||E05||N705||S507||GGACTCCT||AAGGAGTA||AR-150618-Ch74-E05-N705-S507||GGACTCCT-AAGGAGTA||1||live||extravasating | |||
|- | |||
| AR||150618||Ch73||E06||N706||S507||TAGGCATG||AAGGAGTA||AR-150618-Ch73-E06-N706-S507||TAGGCATG-AAGGAGTA||0||na||na | |||
|- | |||
| AR||150618||Ch28||E07||N707||S507||CTCTCTAC||AAGGAGTA||AR-150618-Ch28-E07-N707-S507||CTCTCTAC-AAGGAGTA||1||live||weak | |||
|- | |||
| AR||150618||Ch29||E08||N710||S507||CGAGGCTG||AAGGAGTA||AR-150618-Ch29-E08-N710-S507||CGAGGCTG-AAGGAGTA||1||live||extravasating | |||
|- | |||
| AR||150618||Ch30||E09||N711||S507||AAGAGGCA||AAGGAGTA||AR-150618-Ch30-E09-N711-S507||AAGAGGCA-AAGGAGTA||1||live||weak | |||
|- | |||
| AR||150618||Ch78||E10||N712||S507||GTAGAGGA||AAGGAGTA||AR-150618-Ch78-E10-N712-S507||GTAGAGGA-AAGGAGTA||0||na||na | |||
|- | |||
| AR||150618||Ch77||E11||N714||S507||GCTCATGA||AAGGAGTA||AR-150618-Ch77-E11-N714-S507||GCTCATGA-AAGGAGTA||1||dead||weak | |||
|- | |||
| AR||150618||Ch76||E12||N715||S507||ATCTCAGG||AAGGAGTA||AR-150618-Ch76-E12-N715-S507||ATCTCAGG-AAGGAGTA||0||na||na | |||
|- | |||
| AR||150618||Ch31||F01||N701||S508||TAAGGCGA||CTAAGCCT||AR-150618-Ch31-F01-N701-S508||TAAGGCGA-CTAAGCCT||2||dead||na | |||
|- | |||
| AR||150618||Ch32||F02||N702||S508||CGTACTAG||CTAAGCCT||AR-150618-Ch32-F02-N702-S508||CGTACTAG-CTAAGCCT||0||na||na | |||
|- | |||
| AR||150618||Ch33||F03||N703||S508||AGGCAGAA||CTAAGCCT||AR-150618-Ch33-F03-N703-S508||AGGCAGAA-CTAAGCCT||1||dead||na | |||
|- | |||
| AR||150618||Ch81||F04||N704||S508||TCCTGAGC||CTAAGCCT||AR-150618-Ch81-F04-N704-S508||TCCTGAGC-CTAAGCCT||0||na||na | |||
|- | |||
| AR||150618||Ch80||F05||N705||S508||GGACTCCT||CTAAGCCT||AR-150618-Ch80-F05-N705-S508||GGACTCCT-CTAAGCCT||1||dead||na | |||
|- | |||
| AR||150618||Ch79||F06||N706||S508||TAGGCATG||CTAAGCCT||AR-150618-Ch79-F06-N706-S508||TAGGCATG-CTAAGCCT||1||dead||extravasating | |||
|- | |||
| AR||150618||Ch34||F07||N707||S508||CTCTCTAC||CTAAGCCT||AR-150618-Ch34-F07-N707-S508||CTCTCTAC-CTAAGCCT||1||live||weak | |||
|- | |||
| AR||150618||Ch35||F08||N710||S508||CGAGGCTG||CTAAGCCT||AR-150618-Ch35-F08-N710-S508||CGAGGCTG-CTAAGCCT||2||live||na | |||
|- | |||
| AR||150618||Ch36||F09||N711||S508||AAGAGGCA||CTAAGCCT||AR-150618-Ch36-F09-N711-S508||AAGAGGCA-CTAAGCCT||0||na||na | |||
|- | |||
| AR||150618||Ch84||F10||N712||S508||GTAGAGGA||CTAAGCCT||AR-150618-Ch84-F10-N712-S508||GTAGAGGA-CTAAGCCT||0||na||na | |||
|- | |||
| AR||150618||Ch83||F11||N714||S508||GCTCATGA||CTAAGCCT||AR-150618-Ch83-F11-N714-S508||GCTCATGA-CTAAGCCT||0||na||na | |||
|- | |||
| AR||150618||Ch82||F12||N715||S508||ATCTCAGG||CTAAGCCT||AR-150618-Ch82-F12-N715-S508||ATCTCAGG-CTAAGCCT||1||live||extravasating | |||
|- | |||
| AR||150618||Ch37||G01||N701||S510||TAAGGCGA||CGTCTAAT||AR-150618-Ch37-G01-N701-S510||TAAGGCGA-CGTCTAAT||0||na||na | |||
|- | |||
| AR||150618||Ch38||G02||N702||S510||CGTACTAG||CGTCTAAT||AR-150618-Ch38-G02-N702-S510||CGTACTAG-CGTCTAAT||0||dead||na | |||
|- | |||
| AR||150618||Ch39||G03||N703||S510||AGGCAGAA||CGTCTAAT||AR-150618-Ch39-G03-N703-S510||AGGCAGAA-CGTCTAAT||1||live||na | |||
|- | |||
| AR||150618||Ch87||G04||N704||S510||TCCTGAGC||CGTCTAAT||AR-150618-Ch87-G04-N704-S510||TCCTGAGC-CGTCTAAT||0||na||na | |||
|- | |||
| AR||150618||Ch86||G05||N705||S510||GGACTCCT||CGTCTAAT||AR-150618-Ch86-G05-N705-S510||GGACTCCT-CGTCTAAT||1||dead||na | |||
|- | |||
| AR||150618||Ch85||G06||N706||S510||TAGGCATG||CGTCTAAT||AR-150618-Ch85-G06-N706-S510||TAGGCATG-CGTCTAAT||0||na||na | |||
|- | |||
| AR||150618||Ch40||G07||N707||S510||CTCTCTAC||CGTCTAAT||AR-150618-Ch40-G07-N707-S510||CTCTCTAC-CGTCTAAT||3||dead||na | |||
|- | |||
| AR||150618||Ch41||G08||N710||S510||CGAGGCTG||CGTCTAAT||AR-150618-Ch41-G08-N710-S510||CGAGGCTG-CGTCTAAT||1||dead||na | |||
|- | |||
| AR||150618||Ch42||G09||N711||S510||AAGAGGCA||CGTCTAAT||AR-150618-Ch42-G09-N711-S510||AAGAGGCA-CGTCTAAT||1||dead||extravasating | |||
|- | |||
| AR||150618||Ch90||G10||N712||S510||GTAGAGGA||CGTCTAAT||AR-150618-Ch90-G10-N712-S510||GTAGAGGA-CGTCTAAT||2||both||na | |||
|- | |||
| AR||150618||Ch89||G11||N714||S510||GCTCATGA||CGTCTAAT||AR-150618-Ch89-G11-N714-S510||GCTCATGA-CGTCTAAT||1||both||weak | |||
|- | |||
| AR||150618||Ch88||G12||N715||S510||ATCTCAGG||CGTCTAAT||AR-150618-Ch88-G12-N715-S510||ATCTCAGG-CGTCTAAT||1||dead||na | |||
|- | |||
| AR||150618||Ch43||H01||N701||S511||TAAGGCGA||TCTCTCCG||AR-150618-Ch43-H01-N701-S511||TAAGGCGA-TCTCTCCG||1||dead||extravasating | |||
|- | |||
| AR||150618||Ch44||H02||N702||S511||CGTACTAG||TCTCTCCG||AR-150618-Ch44-H02-N702-S511||CGTACTAG-TCTCTCCG||0||na||debris | |||
|- | |||
| AR||150618||Ch45||H03||N703||S511||AGGCAGAA||TCTCTCCG||AR-150618-Ch45-H03-N703-S511||AGGCAGAA-TCTCTCCG||1||live||extravasating | |||
|- | |||
| AR||150618||Ch93||H04||N704||S511||TCCTGAGC||TCTCTCCG||AR-150618-Ch93-H04-N704-S511||TCCTGAGC-TCTCTCCG||0||na||na | |||
|- | |||
| AR||150618||Ch92||H05||N705||S511||GGACTCCT||TCTCTCCG||AR-150618-Ch92-H05-N705-S511||GGACTCCT-TCTCTCCG||1||live||bright | |||
|- | |||
| AR||150618||Ch91||H06||N706||S511||TAGGCATG||TCTCTCCG||AR-150618-Ch91-H06-N706-S511||TAGGCATG-TCTCTCCG||0||both||debris | |||
|- | |||
| AR||150618||Ch46||H07||N707||S511||CTCTCTAC||TCTCTCCG||AR-150618-Ch46-H07-N707-S511||CTCTCTAC-TCTCTCCG||1||dead||na | |||
|- | |||
| AR||150618||Ch47||H08||N710||S511||CGAGGCTG||TCTCTCCG||AR-150618-Ch47-H08-N710-S511||CGAGGCTG-TCTCTCCG||1||both||extravasating | |||
|- | |||
| AR||150618||Ch48||H09||N711||S511||AAGAGGCA||TCTCTCCG||AR-150618-Ch48-H09-N711-S511||AAGAGGCA-TCTCTCCG||0||na||na | |||
|- | |||
| AR||150618||Ch96||H10||N712||S511||GTAGAGGA||TCTCTCCG||AR-150618-Ch96-H10-N712-S511||GTAGAGGA-TCTCTCCG||1||live||extravasating | |||
|- | |||
| AR||150618||Ch95||H11||N714||S511||GCTCATGA||TCTCTCCG||AR-150618-Ch95-H11-N714-S511||GCTCATGA-TCTCTCCG||1||live||extravasating | |||
|- | |||
| AR||150618||Ch94||H12||N715||S511||ATCTCAGG||TCTCTCCG||AR-150618-Ch94-H12-N715-S511||ATCTCAGG-TCTCTCCG||1||dead||na | |||
|- | |||
| | |||
|} | |||
====Nextera PCR==== | |||
Ran Nextera PCR on Eppendorf qPCR machine | |||
[[File:AR150618_NexteraPCR.png|800px]] | |||
[File:AR150618_C1_gels.png| | ====Size selection==== | ||
[[File:AR150618_C1_gels.png|800px]] | |||
====Sequencing==== | ====Sequencing==== | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Hasty Lab Miseq''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
|- | |||
| Kit Provider: Kun Zhang Lab|||||||||||||||||| | |||
|- | |||
| 6/24/2015|||||||||||||||||| | |||
|- | |||
| Loading Concentration: 26.5 pM|||||||||||||||||| | |||
|- | |||
| Sample ID||Index Sequence||# of Reads||Run Type, Minmum BP||Library Size||Gel Image||Read 1 Sequencing Primer||Index Primer||Read 2 Sequencing Primer||Notes | |||
|- | |||
| INITIAL-PROJECT-SAMPLE-DATE-Index||CGTGCA||Million||SE/PE, 36+6+36||SIZE RANGE (BP)||Link||Name||Name||Name||Labeling, pooling, quantification, etc | |||
|- | |||
| AR-150618-Ch03-A01-N701-S502||TAAGGCGA-CTCTCTAT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch02-A02-N702-S502||CGTACTAG-CTCTCTAT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch07-B03-N703-S503||AGGCAGAA-TATCCTCT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch12-B07-N707-S503||CTCTCTAC-TATCCTCT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch13-C03-N703-S505||AGGCAGAA-GTAAGGAG||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch17-C08-N710-S505||CGAGGCTG-GTAAGGAG||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch21-D01-N701-S506||TAAGGCGA-ACTGCATA||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch20-D02-N702-S506||CGTACTAG-ACTGCATA||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch24-D07-N707-S506||CTCTCTAC-ACTGCATA||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch23-D08-N710-S506||CGAGGCTG-ACTGCATA||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch22-D09-N711-S506||AAGAGGCA-ACTGCATA||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch70-D10-N712-S506||GTAGAGGA-ACTGCATA||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch74-E05-N705-S507||GGACTCCT-AAGGAGTA||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch29-E08-N710-S507||CGAGGCTG-AAGGAGTA||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch33-F03-N703-S508||AGGCAGAA-CTAAGCCT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch80-F05-N705-S508||GGACTCCT-CTAAGCCT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch79-F06-N706-S508||TAGGCATG-CTAAGCCT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch82-F12-N715-S508||ATCTCAGG-CTAAGCCT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch39-G03-N703-S510||AGGCAGAA-CGTCTAAT||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|- | |||
| AR-150618-Ch45-H03-N703-S511||AGGCAGAA-TCTCTCCG||1||SE50+8+8||250-800||http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png||HP10||HP12||NA||Tube labeled AR 6/18 | |||
|} | |||
====Screening==== | |||
[[File:AR150618_libraryComplexities.jpg|800px]] | |||
====CNV profiling==== | |||
[[File:AR-150618-Ch02-A02-N702-S502.all.png|600px]] | |||
[[File:AR-150618-Ch03-A01-N701-S502.all.png|600px]] | |||
[[File:AR-150618-Ch07-B03-N703-S503.all.png|600px]] | |||
[[File:AR-150618-Ch12-B07-N707-S503.all.png|600px]] | |||
[[File:AR-150618-Ch13-C03-N703-S505.all.png|600px]] | |||
[[File:AR-150618-Ch17-C08-N710-S505.all.png|600px]] | |||
[[File:AR-150618-Ch20-D02-N702-S506.all.png|600px]] | |||
[[File:AR-150618-Ch21-D01-N701-S506.all.png|600px]] | |||
[[File:AR-150618-Ch22-D09-N711-S506.all.png|600px]] | |||
[[File:AR-150618-Ch23-D08-N710-S506.all.png|600px]] | |||
[[File:AR-150618-Ch24-D07-N707-S506.all.png|600px]] | |||
[[File:AR-150618-Ch29-E08-N710-S507.all.png|600px]] | |||
[[File:AR-150618-Ch33-F03-N703-S508.all.png|600px]] | |||
[[File:AR-150618-Ch39-G03-N703-S510.all.png|600px]] | |||
[[File:AR-150618-Ch45-H03-N703-S511.all.png|600px]] | |||
[[File:AR-150618-Ch70-D10-N712-S506.all.png|600px]] | |||
[[File:AR-150618-Ch74-E05-N705-S507.all.png|600px]] | |||
[[File:AR-150618-Ch79-F06-N706-S508.all.png|600px]] | |||
[[File:AR-150618-Ch80-F05-N705-S508.all.png|600px]] | |||
[[File:AR-150618-Ch82-F12-N715-S508.all.png|600px]] | |||
====Lorenz Curves==== | |||
[[File:AR-150618-Ch02-A02-N702-S502_lorenz.png|600px]] | |||
[[File:AR-150618-Ch03-A01-N701-S502_lorenz.png|600px]] | |||
[[File:AR-150618-Ch07-B03-N703-S503_lorenz.png|600px]] | |||
[[File:AR-150618-Ch12-B07-N707-S503_lorenz.png|600px]] | |||
[[File:AR-150618-Ch13-C03-N703-S505_lorenz.png|600px]] | |||
[[File:AR-150618-Ch17-C08-N710-S505_lorenz.png|600px]] | |||
[[File:AR-150618-Ch20-D02-N702-S506_lorenz.png|600px]] | |||
[[File:AR-150618-Ch21-D01-N701-S506_lorenz.png|600px]] | |||
[[File:AR-150618-Ch22-D09-N711-S506_lorenz.png|600px]] | |||
[[File:AR-150618-Ch23-D08-N710-S506_lorenz.png|600px]] | |||
[[File:AR-150618-Ch24-D07-N707-S506_lorenz.png|600px]] | |||
[[File:AR-150618-Ch29-E08-N710-S507_lorenz.png|600px]] | |||
[[File:AR-150618-Ch33-F03-N703-S508_lorenz.png|600px]] | |||
[[File:AR-150618-Ch39-G03-N703-S510_lorenz.png|600px]] | |||
[[File:AR-150618-Ch45-H03-N703-S511_lorenz.png|600px]] | |||
[[File:AR-150618-Ch70-D10-N712-S506_lorenz.png|600px]] | |||
[[File:AR-150618-Ch74-E05-N705-S507_lorenz.png|600px]] | |||
[[File:AR-150618-Ch79-F06-N706-S508_lorenz.png|600px]] | |||
[[File:AR-150618-Ch80-F05-N705-S508_lorenz.png|600px]] | |||
[[File:AR-150618-Ch82-F12-N715-S508_lorenz.png|600px]] | |||
====Mouse pipeline==== | |||
Column purified MEF gDNA was used as a cell-free control. It was run through an identical pipeline constructed for mm10 instead of hg38 | |||
[[File:AR150618_mouse_libraryComplexities.jpg|600px]] | |||
[[File:AR-150618-Ch02-A02-N702-S502_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch03-A01-N701-S502_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch07-B03-N703-S503_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch12-B07-N707-S503_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch13-C03-N703-S505_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch17-C08-N710-S505_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch20-D02-N702-S506_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch21-D01-N701-S506_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch22-D09-N711-S506_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch23-D08-N710-S506_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch24-D07-N707-S506_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch29-E08-N710-S507_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch33-F03-N703-S508_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch39-G03-N703-S510_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch45-H03-N703-S511_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch70-D10-N712-S506_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch74-E05-N705-S507_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch79-F06-N706-S508_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch80-F05-N705-S508_mouse.jpg|600px]] | |||
[[File:AR-150618-Ch82-F12-N715-S508_mouse.jpg|600px]] |
Latest revision as of 21:01, 9 September 2015
31 nL MDA on C1 with GM12878[edit]
Overview[edit]
Motivation[edit]
Reagents[edit]
Protocol[edit]
File:Protocol Worksheet AR150618 C1 v1-1.png
File:Protocol Worksheet AR150618 C1 v1-2.png
File:Protocol Worksheet AR150618 C1 v1-3.png
File:AR150618 thermalProfile.png
Results[edit]
Cell capture[edit]
Initials | Date (YYMMDD) | Chamber | Well | i7 | i5 | i7 sequence (RC) | i5 barcode | SampleID | Full barcode | Number | LiveOrDead | Notes |
AR | 150618 | Ch03 | A01 | N701 | S502 | TAAGGCGA | CTCTCTAT | AR-150618-Ch03-A01-N701-S502 | TAAGGCGA-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch02 | A02 | N702 | S502 | CGTACTAG | CTCTCTAT | AR-150618-Ch02-A02-N702-S502 | CGTACTAG-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch01 | A03 | N703 | S502 | AGGCAGAA | CTCTCTAT | AR-150618-Ch01-A03-N703-S502 | AGGCAGAA-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch49 | A04 | N704 | S502 | TCCTGAGC | CTCTCTAT | AR-150618-Ch49-A04-N704-S502 | TCCTGAGC-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch50 | A05 | N705 | S502 | GGACTCCT | CTCTCTAT | AR-150618-Ch50-A05-N705-S502 | GGACTCCT-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch51 | A06 | N706 | S502 | TAGGCATG | CTCTCTAT | AR-150618-Ch51-A06-N706-S502 | TAGGCATG-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch06 | A07 | N707 | S502 | CTCTCTAC | CTCTCTAT | AR-150618-Ch06-A07-N707-S502 | CTCTCTAC-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch05 | A08 | N710 | S502 | CGAGGCTG | CTCTCTAT | AR-150618-Ch05-A08-N710-S502 | CGAGGCTG-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch04 | A09 | N711 | S502 | AAGAGGCA | CTCTCTAT | AR-150618-Ch04-A09-N711-S502 | AAGAGGCA-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch52 | A10 | N712 | S502 | GTAGAGGA | CTCTCTAT | AR-150618-Ch52-A10-N712-S502 | GTAGAGGA-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch53 | A11 | N714 | S502 | GCTCATGA | CTCTCTAT | AR-150618-Ch53-A11-N714-S502 | GCTCATGA-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch54 | A12 | N715 | S502 | ATCTCAGG | CTCTCTAT | AR-150618-Ch54-A12-N715-S502 | ATCTCAGG-CTCTCTAT | 0 | na | na |
AR | 150618 | Ch09 | B01 | N701 | S503 | TAAGGCGA | TATCCTCT | AR-150618-Ch09-B01-N701-S503 | TAAGGCGA-TATCCTCT | 0 | na | na |
AR | 150618 | Ch08 | B02 | N702 | S503 | CGTACTAG | TATCCTCT | AR-150618-Ch08-B02-N702-S503 | CGTACTAG-TATCCTCT | 0 | na | na |
AR | 150618 | Ch07 | B03 | N703 | S503 | AGGCAGAA | TATCCTCT | AR-150618-Ch07-B03-N703-S503 | AGGCAGAA-TATCCTCT | 1 | dead | na |
AR | 150618 | Ch55 | B04 | N704 | S503 | TCCTGAGC | TATCCTCT | AR-150618-Ch55-B04-N704-S503 | TCCTGAGC-TATCCTCT | 0 | na | na |
AR | 150618 | Ch56 | B05 | N705 | S503 | GGACTCCT | TATCCTCT | AR-150618-Ch56-B05-N705-S503 | GGACTCCT-TATCCTCT | 0 | na | na |
AR | 150618 | Ch57 | B06 | N706 | S503 | TAGGCATG | TATCCTCT | AR-150618-Ch57-B06-N706-S503 | TAGGCATG-TATCCTCT | 0 | na | na |
AR | 150618 | Ch12 | B07 | N707 | S503 | CTCTCTAC | TATCCTCT | AR-150618-Ch12-B07-N707-S503 | CTCTCTAC-TATCCTCT | 1 | dead | na |
AR | 150618 | Ch11 | B08 | N710 | S503 | CGAGGCTG | TATCCTCT | AR-150618-Ch11-B08-N710-S503 | CGAGGCTG-TATCCTCT | 3 | dead | na |
AR | 150618 | Ch10 | B09 | N711 | S503 | AAGAGGCA | TATCCTCT | AR-150618-Ch10-B09-N711-S503 | AAGAGGCA-TATCCTCT | 1 | dead | weak |
AR | 150618 | Ch58 | B10 | N712 | S503 | GTAGAGGA | TATCCTCT | AR-150618-Ch58-B10-N712-S503 | GTAGAGGA-TATCCTCT | 0 | na | na |
AR | 150618 | Ch59 | B11 | N714 | S503 | GCTCATGA | TATCCTCT | AR-150618-Ch59-B11-N714-S503 | GCTCATGA-TATCCTCT | 0 | na | na |
AR | 150618 | Ch60 | B12 | N715 | S503 | ATCTCAGG | TATCCTCT | AR-150618-Ch60-B12-N715-S503 | ATCTCAGG-TATCCTCT | 0 | na | na |
AR | 150618 | Ch15 | C01 | N701 | S505 | TAAGGCGA | GTAAGGAG | AR-150618-Ch15-C01-N701-S505 | TAAGGCGA-GTAAGGAG | 2 | dead | na |
AR | 150618 | Ch14 | C02 | N702 | S505 | CGTACTAG | GTAAGGAG | AR-150618-Ch14-C02-N702-S505 | CGTACTAG-GTAAGGAG | 1 | dead | lumpy |
AR | 150618 | Ch13 | C03 | N703 | S505 | AGGCAGAA | GTAAGGAG | AR-150618-Ch13-C03-N703-S505 | AGGCAGAA-GTAAGGAG | 1 | live | extravasating |
AR | 150618 | Ch61 | C04 | N704 | S505 | TCCTGAGC | GTAAGGAG | AR-150618-Ch61-C04-N704-S505 | TCCTGAGC-GTAAGGAG | 1 | dead | weak |
AR | 150618 | Ch62 | C05 | N705 | S505 | GGACTCCT | GTAAGGAG | AR-150618-Ch62-C05-N705-S505 | GGACTCCT-GTAAGGAG | 0 | na | na |
AR | 150618 | Ch63 | C06 | N706 | S505 | TAGGCATG | GTAAGGAG | AR-150618-Ch63-C06-N706-S505 | TAGGCATG-GTAAGGAG | 0 | na | na |
AR | 150618 | Ch18 | C07 | N707 | S505 | CTCTCTAC | GTAAGGAG | AR-150618-Ch18-C07-N707-S505 | CTCTCTAC-GTAAGGAG | 1 | both | extravasating |
AR | 150618 | Ch17 | C08 | N710 | S505 | CGAGGCTG | GTAAGGAG | AR-150618-Ch17-C08-N710-S505 | CGAGGCTG-GTAAGGAG | 1 | live | extravasating |
AR | 150618 | Ch16 | C09 | N711 | S505 | AAGAGGCA | GTAAGGAG | AR-150618-Ch16-C09-N711-S505 | AAGAGGCA-GTAAGGAG | 1 | both | na |
AR | 150618 | Ch64 | C10 | N712 | S505 | GTAGAGGA | GTAAGGAG | AR-150618-Ch64-C10-N712-S505 | GTAGAGGA-GTAAGGAG | 0 | na | na |
AR | 150618 | Ch65 | C11 | N714 | S505 | GCTCATGA | GTAAGGAG | AR-150618-Ch65-C11-N714-S505 | GCTCATGA-GTAAGGAG | 0 | na | na |
AR | 150618 | Ch66 | C12 | N715 | S505 | ATCTCAGG | GTAAGGAG | AR-150618-Ch66-C12-N715-S505 | ATCTCAGG-GTAAGGAG | 0 | na | na |
AR | 150618 | Ch21 | D01 | N701 | S506 | TAAGGCGA | ACTGCATA | AR-150618-Ch21-D01-N701-S506 | TAAGGCGA-ACTGCATA | 1 | live | extravasating |
AR | 150618 | Ch20 | D02 | N702 | S506 | CGTACTAG | ACTGCATA | AR-150618-Ch20-D02-N702-S506 | CGTACTAG-ACTGCATA | 1 | dead | na |
AR | 150618 | Ch19 | D03 | N703 | S506 | AGGCAGAA | ACTGCATA | AR-150618-Ch19-D03-N703-S506 | AGGCAGAA-ACTGCATA | 0 | na | na |
AR | 150618 | Ch67 | D04 | N704 | S506 | TCCTGAGC | ACTGCATA | AR-150618-Ch67-D04-N704-S506 | TCCTGAGC-ACTGCATA | 0 | na | na |
AR | 150618 | Ch68 | D05 | N705 | S506 | GGACTCCT | ACTGCATA | AR-150618-Ch68-D05-N705-S506 | GGACTCCT-ACTGCATA | 0 | na | na |
AR | 150618 | Ch69 | D06 | N706 | S506 | TAGGCATG | ACTGCATA | AR-150618-Ch69-D06-N706-S506 | TAGGCATG-ACTGCATA | 0 | na | na |
AR | 150618 | Ch24 | D07 | N707 | S506 | CTCTCTAC | ACTGCATA | AR-150618-Ch24-D07-N707-S506 | CTCTCTAC-ACTGCATA | 1 | dead | extravasating |
AR | 150618 | Ch23 | D08 | N710 | S506 | CGAGGCTG | ACTGCATA | AR-150618-Ch23-D08-N710-S506 | CGAGGCTG-ACTGCATA | 1 | dead | na |
AR | 150618 | Ch22 | D09 | N711 | S506 | AAGAGGCA | ACTGCATA | AR-150618-Ch22-D09-N711-S506 | AAGAGGCA-ACTGCATA | 1 | live | extravasating |
AR | 150618 | Ch70 | D10 | N712 | S506 | GTAGAGGA | ACTGCATA | AR-150618-Ch70-D10-N712-S506 | GTAGAGGA-ACTGCATA | 1 | dead | extravasating |
AR | 150618 | Ch71 | D11 | N714 | S506 | GCTCATGA | ACTGCATA | AR-150618-Ch71-D11-N714-S506 | GCTCATGA-ACTGCATA | 0 | na | na |
AR | 150618 | Ch72 | D12 | N715 | S506 | ATCTCAGG | ACTGCATA | AR-150618-Ch72-D12-N715-S506 | ATCTCAGG-ACTGCATA | 0 | na | na |
AR | 150618 | Ch25 | E01 | N701 | S507 | TAAGGCGA | AAGGAGTA | AR-150618-Ch25-E01-N701-S507 | TAAGGCGA-AAGGAGTA | 1 | live | weak |
AR | 150618 | Ch26 | E02 | N702 | S507 | CGTACTAG | AAGGAGTA | AR-150618-Ch26-E02-N702-S507 | CGTACTAG-AAGGAGTA | 0 | na | na |
AR | 150618 | Ch27 | E03 | N703 | S507 | AGGCAGAA | AAGGAGTA | AR-150618-Ch27-E03-N703-S507 | AGGCAGAA-AAGGAGTA | 0 | na | na |
AR | 150618 | Ch75 | E04 | N704 | S507 | TCCTGAGC | AAGGAGTA | AR-150618-Ch75-E04-N704-S507 | TCCTGAGC-AAGGAGTA | 0 | na | na |
AR | 150618 | Ch74 | E05 | N705 | S507 | GGACTCCT | AAGGAGTA | AR-150618-Ch74-E05-N705-S507 | GGACTCCT-AAGGAGTA | 1 | live | extravasating |
AR | 150618 | Ch73 | E06 | N706 | S507 | TAGGCATG | AAGGAGTA | AR-150618-Ch73-E06-N706-S507 | TAGGCATG-AAGGAGTA | 0 | na | na |
AR | 150618 | Ch28 | E07 | N707 | S507 | CTCTCTAC | AAGGAGTA | AR-150618-Ch28-E07-N707-S507 | CTCTCTAC-AAGGAGTA | 1 | live | weak |
AR | 150618 | Ch29 | E08 | N710 | S507 | CGAGGCTG | AAGGAGTA | AR-150618-Ch29-E08-N710-S507 | CGAGGCTG-AAGGAGTA | 1 | live | extravasating |
AR | 150618 | Ch30 | E09 | N711 | S507 | AAGAGGCA | AAGGAGTA | AR-150618-Ch30-E09-N711-S507 | AAGAGGCA-AAGGAGTA | 1 | live | weak |
AR | 150618 | Ch78 | E10 | N712 | S507 | GTAGAGGA | AAGGAGTA | AR-150618-Ch78-E10-N712-S507 | GTAGAGGA-AAGGAGTA | 0 | na | na |
AR | 150618 | Ch77 | E11 | N714 | S507 | GCTCATGA | AAGGAGTA | AR-150618-Ch77-E11-N714-S507 | GCTCATGA-AAGGAGTA | 1 | dead | weak |
AR | 150618 | Ch76 | E12 | N715 | S507 | ATCTCAGG | AAGGAGTA | AR-150618-Ch76-E12-N715-S507 | ATCTCAGG-AAGGAGTA | 0 | na | na |
AR | 150618 | Ch31 | F01 | N701 | S508 | TAAGGCGA | CTAAGCCT | AR-150618-Ch31-F01-N701-S508 | TAAGGCGA-CTAAGCCT | 2 | dead | na |
AR | 150618 | Ch32 | F02 | N702 | S508 | CGTACTAG | CTAAGCCT | AR-150618-Ch32-F02-N702-S508 | CGTACTAG-CTAAGCCT | 0 | na | na |
AR | 150618 | Ch33 | F03 | N703 | S508 | AGGCAGAA | CTAAGCCT | AR-150618-Ch33-F03-N703-S508 | AGGCAGAA-CTAAGCCT | 1 | dead | na |
AR | 150618 | Ch81 | F04 | N704 | S508 | TCCTGAGC | CTAAGCCT | AR-150618-Ch81-F04-N704-S508 | TCCTGAGC-CTAAGCCT | 0 | na | na |
AR | 150618 | Ch80 | F05 | N705 | S508 | GGACTCCT | CTAAGCCT | AR-150618-Ch80-F05-N705-S508 | GGACTCCT-CTAAGCCT | 1 | dead | na |
AR | 150618 | Ch79 | F06 | N706 | S508 | TAGGCATG | CTAAGCCT | AR-150618-Ch79-F06-N706-S508 | TAGGCATG-CTAAGCCT | 1 | dead | extravasating |
AR | 150618 | Ch34 | F07 | N707 | S508 | CTCTCTAC | CTAAGCCT | AR-150618-Ch34-F07-N707-S508 | CTCTCTAC-CTAAGCCT | 1 | live | weak |
AR | 150618 | Ch35 | F08 | N710 | S508 | CGAGGCTG | CTAAGCCT | AR-150618-Ch35-F08-N710-S508 | CGAGGCTG-CTAAGCCT | 2 | live | na |
AR | 150618 | Ch36 | F09 | N711 | S508 | AAGAGGCA | CTAAGCCT | AR-150618-Ch36-F09-N711-S508 | AAGAGGCA-CTAAGCCT | 0 | na | na |
AR | 150618 | Ch84 | F10 | N712 | S508 | GTAGAGGA | CTAAGCCT | AR-150618-Ch84-F10-N712-S508 | GTAGAGGA-CTAAGCCT | 0 | na | na |
AR | 150618 | Ch83 | F11 | N714 | S508 | GCTCATGA | CTAAGCCT | AR-150618-Ch83-F11-N714-S508 | GCTCATGA-CTAAGCCT | 0 | na | na |
AR | 150618 | Ch82 | F12 | N715 | S508 | ATCTCAGG | CTAAGCCT | AR-150618-Ch82-F12-N715-S508 | ATCTCAGG-CTAAGCCT | 1 | live | extravasating |
AR | 150618 | Ch37 | G01 | N701 | S510 | TAAGGCGA | CGTCTAAT | AR-150618-Ch37-G01-N701-S510 | TAAGGCGA-CGTCTAAT | 0 | na | na |
AR | 150618 | Ch38 | G02 | N702 | S510 | CGTACTAG | CGTCTAAT | AR-150618-Ch38-G02-N702-S510 | CGTACTAG-CGTCTAAT | 0 | dead | na |
AR | 150618 | Ch39 | G03 | N703 | S510 | AGGCAGAA | CGTCTAAT | AR-150618-Ch39-G03-N703-S510 | AGGCAGAA-CGTCTAAT | 1 | live | na |
AR | 150618 | Ch87 | G04 | N704 | S510 | TCCTGAGC | CGTCTAAT | AR-150618-Ch87-G04-N704-S510 | TCCTGAGC-CGTCTAAT | 0 | na | na |
AR | 150618 | Ch86 | G05 | N705 | S510 | GGACTCCT | CGTCTAAT | AR-150618-Ch86-G05-N705-S510 | GGACTCCT-CGTCTAAT | 1 | dead | na |
AR | 150618 | Ch85 | G06 | N706 | S510 | TAGGCATG | CGTCTAAT | AR-150618-Ch85-G06-N706-S510 | TAGGCATG-CGTCTAAT | 0 | na | na |
AR | 150618 | Ch40 | G07 | N707 | S510 | CTCTCTAC | CGTCTAAT | AR-150618-Ch40-G07-N707-S510 | CTCTCTAC-CGTCTAAT | 3 | dead | na |
AR | 150618 | Ch41 | G08 | N710 | S510 | CGAGGCTG | CGTCTAAT | AR-150618-Ch41-G08-N710-S510 | CGAGGCTG-CGTCTAAT | 1 | dead | na |
AR | 150618 | Ch42 | G09 | N711 | S510 | AAGAGGCA | CGTCTAAT | AR-150618-Ch42-G09-N711-S510 | AAGAGGCA-CGTCTAAT | 1 | dead | extravasating |
AR | 150618 | Ch90 | G10 | N712 | S510 | GTAGAGGA | CGTCTAAT | AR-150618-Ch90-G10-N712-S510 | GTAGAGGA-CGTCTAAT | 2 | both | na |
AR | 150618 | Ch89 | G11 | N714 | S510 | GCTCATGA | CGTCTAAT | AR-150618-Ch89-G11-N714-S510 | GCTCATGA-CGTCTAAT | 1 | both | weak |
AR | 150618 | Ch88 | G12 | N715 | S510 | ATCTCAGG | CGTCTAAT | AR-150618-Ch88-G12-N715-S510 | ATCTCAGG-CGTCTAAT | 1 | dead | na |
AR | 150618 | Ch43 | H01 | N701 | S511 | TAAGGCGA | TCTCTCCG | AR-150618-Ch43-H01-N701-S511 | TAAGGCGA-TCTCTCCG | 1 | dead | extravasating |
AR | 150618 | Ch44 | H02 | N702 | S511 | CGTACTAG | TCTCTCCG | AR-150618-Ch44-H02-N702-S511 | CGTACTAG-TCTCTCCG | 0 | na | debris |
AR | 150618 | Ch45 | H03 | N703 | S511 | AGGCAGAA | TCTCTCCG | AR-150618-Ch45-H03-N703-S511 | AGGCAGAA-TCTCTCCG | 1 | live | extravasating |
AR | 150618 | Ch93 | H04 | N704 | S511 | TCCTGAGC | TCTCTCCG | AR-150618-Ch93-H04-N704-S511 | TCCTGAGC-TCTCTCCG | 0 | na | na |
AR | 150618 | Ch92 | H05 | N705 | S511 | GGACTCCT | TCTCTCCG | AR-150618-Ch92-H05-N705-S511 | GGACTCCT-TCTCTCCG | 1 | live | bright |
AR | 150618 | Ch91 | H06 | N706 | S511 | TAGGCATG | TCTCTCCG | AR-150618-Ch91-H06-N706-S511 | TAGGCATG-TCTCTCCG | 0 | both | debris |
AR | 150618 | Ch46 | H07 | N707 | S511 | CTCTCTAC | TCTCTCCG | AR-150618-Ch46-H07-N707-S511 | CTCTCTAC-TCTCTCCG | 1 | dead | na |
AR | 150618 | Ch47 | H08 | N710 | S511 | CGAGGCTG | TCTCTCCG | AR-150618-Ch47-H08-N710-S511 | CGAGGCTG-TCTCTCCG | 1 | both | extravasating |
AR | 150618 | Ch48 | H09 | N711 | S511 | AAGAGGCA | TCTCTCCG | AR-150618-Ch48-H09-N711-S511 | AAGAGGCA-TCTCTCCG | 0 | na | na |
AR | 150618 | Ch96 | H10 | N712 | S511 | GTAGAGGA | TCTCTCCG | AR-150618-Ch96-H10-N712-S511 | GTAGAGGA-TCTCTCCG | 1 | live | extravasating |
AR | 150618 | Ch95 | H11 | N714 | S511 | GCTCATGA | TCTCTCCG | AR-150618-Ch95-H11-N714-S511 | GCTCATGA-TCTCTCCG | 1 | live | extravasating |
AR | 150618 | Ch94 | H12 | N715 | S511 | ATCTCAGG | TCTCTCCG | AR-150618-Ch94-H12-N715-S511 | ATCTCAGG-TCTCTCCG | 1 | dead | na |
Nextera PCR[edit]
Ran Nextera PCR on Eppendorf qPCR machine
Size selection[edit]
Sequencing[edit]
Hasty Lab Miseq | ' | ' | ' | ' | ' | ' | ' | ' | ' |
Kit Provider: Kun Zhang Lab | |||||||||
6/24/2015 | |||||||||
Loading Concentration: 26.5 pM | |||||||||
Sample ID | Index Sequence | # of Reads | Run Type, Minmum BP | Library Size | Gel Image | Read 1 Sequencing Primer | Index Primer | Read 2 Sequencing Primer | Notes |
INITIAL-PROJECT-SAMPLE-DATE-Index | CGTGCA | Million | SE/PE, 36+6+36 | SIZE RANGE (BP) | Link | Name | Name | Name | Labeling, pooling, quantification, etc |
AR-150618-Ch03-A01-N701-S502 | TAAGGCGA-CTCTCTAT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch02-A02-N702-S502 | CGTACTAG-CTCTCTAT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch07-B03-N703-S503 | AGGCAGAA-TATCCTCT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch12-B07-N707-S503 | CTCTCTAC-TATCCTCT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch13-C03-N703-S505 | AGGCAGAA-GTAAGGAG | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch17-C08-N710-S505 | CGAGGCTG-GTAAGGAG | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch21-D01-N701-S506 | TAAGGCGA-ACTGCATA | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch20-D02-N702-S506 | CGTACTAG-ACTGCATA | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch24-D07-N707-S506 | CTCTCTAC-ACTGCATA | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch23-D08-N710-S506 | CGAGGCTG-ACTGCATA | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch22-D09-N711-S506 | AAGAGGCA-ACTGCATA | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch70-D10-N712-S506 | GTAGAGGA-ACTGCATA | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch74-E05-N705-S507 | GGACTCCT-AAGGAGTA | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch29-E08-N710-S507 | CGAGGCTG-AAGGAGTA | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch33-F03-N703-S508 | AGGCAGAA-CTAAGCCT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch80-F05-N705-S508 | GGACTCCT-CTAAGCCT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch79-F06-N706-S508 | TAGGCATG-CTAAGCCT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch82-F12-N715-S508 | ATCTCAGG-CTAAGCCT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch39-G03-N703-S510 | AGGCAGAA-CGTCTAAT | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
AR-150618-Ch45-H03-N703-S511 | AGGCAGAA-TCTCTCCG | 1 | SE50+8+8 | 250-800 | http://genome-tech.ucsd.edu/LabNotes/index.php/File:AR150618_C1_gels.png | HP10 | HP12 | NA | Tube labeled AR 6/18 |
Screening[edit]
File:AR150618 libraryComplexities.jpg
CNV profiling[edit]
File:AR-150618-Ch02-A02-N702-S502.all.png File:AR-150618-Ch03-A01-N701-S502.all.png File:AR-150618-Ch07-B03-N703-S503.all.png File:AR-150618-Ch12-B07-N707-S503.all.png File:AR-150618-Ch13-C03-N703-S505.all.png File:AR-150618-Ch17-C08-N710-S505.all.png File:AR-150618-Ch20-D02-N702-S506.all.png File:AR-150618-Ch21-D01-N701-S506.all.png File:AR-150618-Ch22-D09-N711-S506.all.png File:AR-150618-Ch23-D08-N710-S506.all.png File:AR-150618-Ch24-D07-N707-S506.all.png File:AR-150618-Ch29-E08-N710-S507.all.png File:AR-150618-Ch33-F03-N703-S508.all.png File:AR-150618-Ch39-G03-N703-S510.all.png File:AR-150618-Ch45-H03-N703-S511.all.png File:AR-150618-Ch70-D10-N712-S506.all.png File:AR-150618-Ch74-E05-N705-S507.all.png File:AR-150618-Ch79-F06-N706-S508.all.png File:AR-150618-Ch80-F05-N705-S508.all.png File:AR-150618-Ch82-F12-N715-S508.all.png
Lorenz Curves[edit]
File:AR-150618-Ch02-A02-N702-S502 lorenz.png File:AR-150618-Ch03-A01-N701-S502 lorenz.png File:AR-150618-Ch07-B03-N703-S503 lorenz.png File:AR-150618-Ch12-B07-N707-S503 lorenz.png File:AR-150618-Ch13-C03-N703-S505 lorenz.png File:AR-150618-Ch17-C08-N710-S505 lorenz.png File:AR-150618-Ch20-D02-N702-S506 lorenz.png File:AR-150618-Ch21-D01-N701-S506 lorenz.png File:AR-150618-Ch22-D09-N711-S506 lorenz.png File:AR-150618-Ch23-D08-N710-S506 lorenz.png File:AR-150618-Ch24-D07-N707-S506 lorenz.png File:AR-150618-Ch29-E08-N710-S507 lorenz.png File:AR-150618-Ch33-F03-N703-S508 lorenz.png File:AR-150618-Ch39-G03-N703-S510 lorenz.png File:AR-150618-Ch45-H03-N703-S511 lorenz.png File:AR-150618-Ch70-D10-N712-S506 lorenz.png File:AR-150618-Ch74-E05-N705-S507 lorenz.png File:AR-150618-Ch79-F06-N706-S508 lorenz.png File:AR-150618-Ch80-F05-N705-S508 lorenz.png File:AR-150618-Ch82-F12-N715-S508 lorenz.png
Mouse pipeline[edit]
Column purified MEF gDNA was used as a cell-free control. It was run through an identical pipeline constructed for mm10 instead of hg38
File:AR150618 mouse libraryComplexities.jpg
File:AR-150618-Ch02-A02-N702-S502 mouse.jpg File:AR-150618-Ch03-A01-N701-S502 mouse.jpg File:AR-150618-Ch07-B03-N703-S503 mouse.jpg File:AR-150618-Ch12-B07-N707-S503 mouse.jpg File:AR-150618-Ch13-C03-N703-S505 mouse.jpg File:AR-150618-Ch17-C08-N710-S505 mouse.jpg File:AR-150618-Ch20-D02-N702-S506 mouse.jpg File:AR-150618-Ch21-D01-N701-S506 mouse.jpg File:AR-150618-Ch22-D09-N711-S506 mouse.jpg File:AR-150618-Ch23-D08-N710-S506 mouse.jpg File:AR-150618-Ch24-D07-N707-S506 mouse.jpg File:AR-150618-Ch29-E08-N710-S507 mouse.jpg File:AR-150618-Ch33-F03-N703-S508 mouse.jpg File:AR-150618-Ch39-G03-N703-S510 mouse.jpg File:AR-150618-Ch45-H03-N703-S511 mouse.jpg File:AR-150618-Ch70-D10-N712-S506 mouse.jpg File:AR-150618-Ch74-E05-N705-S507 mouse.jpg File:AR-150618-Ch79-F06-N706-S508 mouse.jpg File:AR-150618-Ch80-F05-N705-S508 mouse.jpg File:AR-150618-Ch82-F12-N715-S508 mouse.jpg