Andrew:Notebook/AR150625 C1

From ZhangLabWiki
Jump to navigation Jump to search

Motivation[edit]

Before we saw the poor results of 31 nL MDA from 6/18, we jumped ahead to Dana's samples using the same protocol.

Dana Tsui's ovarian cancer lines: PEO1 (pre-platinum resistance) and PEO4 (post-platinum resistance)

Same protocol as 6/18/2015

Results[edit]

C1 cell capture[edit]

Chamber Well Number LiveOrDead Notes
Ch03 A01 single dead na
Ch02 A02 empty na na
Ch01 A03 single dead na
Ch49 A04 multiple dead na
Ch50 A05 multiple dead na
Ch51 A06 single dead na
Ch06 A07 multiple dead na
Ch05 A08 empty dead fragment
Ch04 A09 empty na na
Ch52 A10 single dead na
Ch53 A11 multiple dead na
Ch54 A12 single dead na
Ch09 B01 empty na na
Ch08 B02 multiple dead fragment
Ch07 B03 single dead na
Ch55 B04 multiple dead na
Ch56 B05 single dead na
Ch57 B06 empty na na
Ch12 B07 single both na
Ch11 B08 single both na
Ch10 B09 single dead na
Ch58 B10 single dead na
Ch59 B11 multiple dead na
Ch60 B12 single dead na
Ch15 C01 multiple na na
Ch14 C02 empty dead fragment
Ch13 C03 single dead na
Ch61 C04 multiple dead na
Ch62 C05 single dead na
Ch63 C06 empty na na
Ch18 C07 single dead na
Ch17 C08 multiple na na
Ch16 C09 empty na na
Ch64 C10 empty na fragment
Ch65 C11 single dead na
Ch66 C12 multiple dead na
Ch21 D01 empty both fragment
Ch20 D02 single both na
Ch19 D03 empty na na
Ch67 D04 multiple dead na
Ch68 D05 empty na na
Ch69 D06 single dead na
Ch24 D07 single dead na
Ch23 D08 single both na
Ch22 D09 single dead na
Ch70 D10 single dead na
Ch71 D11 single dead na
Ch72 D12 empty na fragment
Ch25 E01 single both na
Ch26 E02 empty na na
Ch27 E03 single both na
Ch75 E04 multiple both na
Ch74 E05 empty na na
Ch73 E06 empty dead fragment
Ch28 E07 empty na na
Ch29 E08 single both na
Ch30 E09 empty na na
Ch78 E10 multiple dead na
Ch77 E11 single both na
Ch76 E12 multiple dead na
Ch31 F01 single both na
Ch32 F02 empty na na
Ch33 F03 single dead na
Ch81 F04 multiple dead na
Ch80 F05 multiple dead na
Ch79 F06 single live weak
Ch34 F07 single dead na
Ch35 F08 multiple both na
Ch36 F09 single live weak
Ch84 F10 single dead na
Ch83 F11 single both na
Ch82 F12 single dead na
Ch37 G01 single both na
Ch38 G02 empty na na
Ch39 G03 empty dead fragment
Ch87 G04 empty dead fragment
Ch86 G05 multiple dead na
Ch85 G06 single both na
Ch40 G07 single dead na
Ch41 G08 multiple dead na
Ch42 G09 empty both fragment
Ch90 G10 multiple dead na
Ch89 G11 single both na
Ch88 G12 empty na na
Ch43 H01 multiple dead na
Ch44 H02 multiple dead na
Ch45 H03 empty na debris
Ch93 H04 single dead na
Ch92 H05 multiple dead na
Ch91 H06 empty na na
Ch46 H07 single dead na
Ch47 H08 empty na na
Ch48 H09 multiple dead na
Ch96 H10 empty dead fragment
Ch95 H11 single both na
Ch94 H12 multiple dead na

Library prep[edit]

File:AR150625 qPCR.jpg

Sequencing[edit]

Hasty Lab Miseq June 29, 2015 Kit Provider: Kun Zhang Lab 27.5 pM loading concentration

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-DATE-PROJECT-SAMPLE-INDEX CGTGCA Million SE/PE, 36+6+36 SIZE RANGE (BP) Link Name Name Name
AR-150625-Ch60-B12-N715-S503 ATCTCAGG-TATCCTCT 2 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled DT 6/29
AR-150625-1mPEO1-A04-N704-S502 TCCTGAGC-CTCTCTAT 2 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Bulk
AR-150625-1mPEO4-A05-N705-S502 GGACTCCT-CTCTCTAT 2 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Bulk
AR-150625-Ch03-A01-N701-S502 TAAGGCGA-CTCTCTAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch02-A02-N702-S502 CGTACTAG-CTCTCTAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch01-A03-N703-S502 AGGCAGAA-CTCTCTAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch51-A06-N706-S502 TAGGCATG-CTCTCTAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch04-A09-N711-S502 AAGAGGCA-CTCTCTAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch52-A10-N712-S502 GTAGAGGA-CTCTCTAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch54-A12-N715-S502 ATCTCAGG-CTCTCTAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch07-B03-N703-S503 AGGCAGAA-TATCCTCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch56-B05-N705-S503 GGACTCCT-TATCCTCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch12-B07-N707-S503 CTCTCTAC-TATCCTCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch11-B08-N710-S503 CGAGGCTG-TATCCTCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch10-B09-N711-S503 AAGAGGCA-TATCCTCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch58-B10-N712-S503 GTAGAGGA-TATCCTCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch13-C03-N703-S505 AGGCAGAA-GTAAGGAG 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch62-C05-N705-S505 GGACTCCT-GTAAGGAG 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch18-C07-N707-S505 CTCTCTAC-GTAAGGAG 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch65-C11-N714-S505 GCTCATGA-GTAAGGAG 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch20-D02-N702-S506 CGTACTAG-ACTGCATA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch69-D06-N706-S506 TAGGCATG-ACTGCATA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch24-D07-N707-S506 CTCTCTAC-ACTGCATA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch23-D08-N710-S506 CGAGGCTG-ACTGCATA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch22-D09-N711-S506 AAGAGGCA-ACTGCATA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch70-D10-N712-S506 GTAGAGGA-ACTGCATA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch71-D11-N714-S506 GCTCATGA-ACTGCATA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch25-E01-N701-S507 TAAGGCGA-AAGGAGTA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch27-E03-N703-S507 AGGCAGAA-AAGGAGTA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch29-E08-N710-S507 CGAGGCTG-AAGGAGTA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch77-E11-N714-S507 GCTCATGA-AAGGAGTA 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch31-F01-N701-S508 TAAGGCGA-CTAAGCCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch33-F03-N703-S508 AGGCAGAA-CTAAGCCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch79-F06-N706-S508 TAGGCATG-CTAAGCCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch34-F07-N707-S508 CTCTCTAC-CTAAGCCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch36-F09-N711-S508 AAGAGGCA-CTAAGCCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch84-F10-N712-S508 GTAGAGGA-CTAAGCCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch83-F11-N714-S508 GCTCATGA-CTAAGCCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch82-F12-N715-S508 ATCTCAGG-CTAAGCCT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch37-G01-N701-S510 TAAGGCGA-CGTCTAAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch85-G06-N706-S510 TAGGCATG-CGTCTAAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch40-G07-N707-S510 CTCTCTAC-CGTCTAAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch89-G11-N714-S510 GCTCATGA-CGTCTAAT 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch93-H04-N704-S511 TCCTGAGC-TCTCTCCG 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch46-H07-N707-S511 CTCTCTAC-TCTCTCCG 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
AR-150625-Ch95-H11-N714-S511 GCTCATGA-TCTCTCCG 0.33 SE50+8+8 250-800 soon HP10 HP12 NA Tube labeled AR 6/26 Single
Total
20.19

File:AR150625 stats.jpg

Screening[edit]

File:AR150625 libraryComplexities.jpg

CNV profiling[edit]

Run had very low yield, most libraries did not have enough reads to make meaningful conclusions. Overall, the noise level seems similar to the 6/18 experiment

File:AR-150625-Ch60-B12-N715-S503.jpg