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Sample GSM1649614 Query DataSets for GSM1649614
Status Public on Oct 01, 2015
Title 196
Sample type genomic
 
Source name swine, tonsils
Organism Yersinia enterocolitica
Characteristics bioserotype: 4/O:3
origin: Finland
Treatment protocol NA
Growth protocol Frozen strains were first grown on blood agar under aerobic conditions at 28°C 24 h. To prepare for DNA isolation the strains were grown in TSB-medium at 28°C 24 h.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted as described by Pitcher et al. (1989). DNA quality was checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)
Label Cy5
Label protocol DNA was labeled using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. Labeled DNA was purified with the DNA purification kit (QIAquick PCR Purification Kit, Qiagen, Hilden, Germany). The concentration of DNA and the incorporation of the dye were checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)
 
Hybridization protocol Agilent (Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.
Scan protocol GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2.
Description 253640110007_3_3.gpr
Data processing Images were processed and checked manually using GenePix Pro 6.0/6.1 software. For data analysis R software LIMMA-package (Smyth et al 2005) was used. Background intensities were fixed using normexp-algorithm (threshold 50).
 
Submission date Apr 03, 2015
Last update date Oct 01, 2015
Contact name Kaisa Aulikki Jaakkola
E-mail(s) kaisa.jaakkola@gmail.com
Organization name University of Helsinki, Faculty of veterinary medicine
Department The Department of Food Hygiene and Environmental Health
Street address Agnes Sjöbergin katu 2
City University of Helsinki
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL19993
Series (1)
GSE67565 Comparative genome hybridization of Enteropathogenic Yersinia

Data table header descriptions
ID_REF
VALUE log2-background corrected intensity, manually checked to follow normal log2 distribution pattern

Data table
ID_REF VALUE
CAL12325.1-15mismatch_1_72_32 6.344338
CAL12325.1-1mismatch_1_93_14 9.313455
CAL12325.1-2mismatch_1_111_53 9.117
CAL12325.1-3mismatch_1_155_26 8.804945
CAL12325.1-4mismatch_1_19_62 8.418917
CAL12325.1-5mismatch_1_86_23 8.51275
CAL12325.1-6mismatch_1_112_96 8.323065
CAL12325.1-7mismatch_1_20_31 8.062059
CAL12325.1-8mismatch_1_119_26 7.763228
CAL12325.1-9mismatch_1_125_78 7.436731
CAL13917.1-15mismatch_1_68_85 6.214394
CAL13917.1-1mismatch_1_65_89 10.73915
CAL13917.1-2mismatch_1_13_9 10.576723
CAL13917.1-3mismatch_1_31_9 10.498104
CAL13917.1-4mismatch_1_38_67 10.524789
CAL13917.1-5mismatch_1_24_22 10.307488
CAL13917.1-6mismatch_1_147_90 9.870754
CAL13917.1-7mismatch_1_118_69 9.781773
CAL13917.1-8mismatch_1_95_51 10.285694
CAL13917.1-9mismatch_1_3_61 9.638893

Total number of rows: 11569

Table truncated, full table size 558 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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