Andrew:Notebook/AR150625 C1: Difference between revisions
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[[File:AR150625_libraryComplexities.jpg|600px]] | [[File:AR150625_libraryComplexities.jpg|600px]] | ||
===CNV profiling=== | |||
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|600px]] |
Latest revision as of 19:41, 10 September 2015
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)
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]
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 | |||||||||
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