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Sample GSM176636 Query DataSets for GSM176636
Status Public on Oct 11, 2007
Title Neisseria meningitidis isolate A342-1
Sample type genomic
 
Channel 1
Source name menA 342
Organism Neisseria meningitidis
Characteristics Neisseria meningitidis Serogroup A isolate
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted by using Wizard Genomic DNA Purification Kit (Promega)
Label Cy5
Label protocol Genomic DNA was fluorescently labeled by random priming with the Klenow fragment.
 
Channel 2
Source name menC 053442
Organism Neisseria meningitidis
Characteristics Neisseria meningitidis Serogroup C isolate (ST4821)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted by using Wizard Genomic DNA Purification Kit (Promega)
Label Cy3
Label protocol Genomic DNA was fluorescently labeled by random priming with the Klenow fragment.
 
 
Hybridization protocol Samples were hybridized overnight at 65°C.
Scan protocol The processed slides were scanned with a GenePix 4000B
scanner (Axon). Fluorescent spots and the local background
intensities were quantified with GenePix Pro 5.0 software (Axon).
Description CGH
Data processing MIDAS (TIGR) & GACK (Genomotyping Analysis by Charlie Kim, Genome Biology 2002)
 
Submission date Mar 20, 2007
Last update date Oct 10, 2007
Contact name Junping Peng
E-mail(s) pengjp@gmail.com
Organization name Chinese center for disease control and prevention
Lab State key lab for molecular virology and genetic engineering
Street address No 6, Rongjing Eastern Street, BDA
City Beijing
ZIP/Postal code 100176
Country China
 
Platform ID GPL5011
Series (1)
GSE7331 CGH result of Neisseria meningitidis ST-7 isolates

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE
BkgA B532 Median
BkgB B635 Median
IA F532 Median
IB F635 Median
PRE_VALUE Ratio of median (635/532)

Data table
ID_REF VALUE BkgA BkgB IA IB PRE_VALUE
1 47840 16100 0 0 0
2 -0.053306382 46920 16100 4845640 4669865 0.963725122
3 0.016536869 45080 16560 2929280 2963050 1.01152843
4 -0.079308585 44620 16560 3647340 3452248 0.946511156
5 -0.216481745 44620 16100 3551200 3056382 0.860661748
6 1.496043762 50220 18900 540000 1523168 2.820681481
7 0.24078516 51300 19980 2505060 2960068 1.18163557
8 0.106559254 51840 19980 2548260 2743603 1.076657405
9 0.077618766 42320 17020 1434740 1514045 1.055274823
10 0.291190097 41860 16560 2653740 3247247 1.223649265
11 0.268207028 42320 16560 2098980 2527823 1.204310189
12 42780 16560 0 0 0
13 0.30196674 49140 19440 2491020 3070989 1.232823903
14 0.507895291 49680 19440 2108700 2998517 1.421974202
15 0.064684409 49140 19980 4046220 4231764 1.045856132
16 -0.031688471 49680 19980 4012740 3925562 0.978274695
17 0.425148815 43240 17020 2690080 3612000 1.342710997
18 0.078417678 44160 17020 3565920 3765110 1.055859357
325 0.057058539 52380 19980 3829140 3983617 1.040342479
326 0.745202788 63024 24336 3601728 6037252 1.676209864

Total number of rows: 2592

Table truncated, full table size 119 Kbytes.




Supplementary data files not provided

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