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Sample GSM1649662 Query DataSets for GSM1649662
Status Public on Oct 01, 2015
Title 297
Sample type genomic
 
Source name swine, carcass
Organism Yersinia enterocolitica
Characteristics bioserotype: 1A
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 253640110002_8_4.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 6.985056
CAL12325.1-1mismatch_1_93_14 13.084614
CAL12325.1-2mismatch_1_111_53 13.034598
CAL12325.1-3mismatch_1_155_26 12.220328
CAL12325.1-4mismatch_1_19_62 11.797594
CAL12325.1-5mismatch_1_86_23 12.33646
CAL12325.1-6mismatch_1_112_96 11.734215
CAL12325.1-7mismatch_1_20_31 11.269613
CAL12325.1-8mismatch_1_119_26 10.764732
CAL12325.1-9mismatch_1_125_78 10.093856
CAL13917.1-15mismatch_1_68_85 6.658295
CAL13917.1-1mismatch_1_65_89 13.453635
CAL13917.1-2mismatch_1_13_9 13.389878
CAL13917.1-3mismatch_1_31_9 13.206684
CAL13917.1-4mismatch_1_38_67 12.859696
CAL13917.1-5mismatch_1_24_22 12.513193
CAL13917.1-6mismatch_1_147_90 12.003459
CAL13917.1-7mismatch_1_118_69 12.273455
CAL13917.1-8mismatch_1_95_51 12.22997
CAL13917.1-9mismatch_1_3_61 10.904508

Total number of rows: 11569

Table truncated, full table size 559 Kbytes.




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

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