Andrew:Notebook/AR150618 C1: Difference between revisions

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==31 nL MDA on C1 with GM12878==
==31 nL MDA on C1 with GM12878==


[[File:AR150618_motivation.png|2000px]]
===Overview===
 
====Motivation====
 
[[File:AR150618_motivation.png|1500px]]
 
====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===
 
====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]]
 
====Size selection====
 
[[File:AR150618_C1_gels.png|800px]]
 
====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]

File:AR150618 motivation.png

Reagents[edit]

File:AR150618 reagents.jpg

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

File:AR150618 NexteraPCR.png

Size selection[edit]

File:AR150618 C1 gels.png

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