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Sample GSM1649646 Query DataSets for GSM1649646
Status Public on Oct 01, 2015
Title 229
Sample type genomic
 
Source name swine, tonsils
Organism Yersinia enterocolitica
Characteristics bioserotype: BT 4
origin: Estonia
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 Cy3
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 253640110004_6_8.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 8.518208
CAL12325.1-1mismatch_1_93_14 11.765698
CAL12325.1-2mismatch_1_111_53 11.719814
CAL12325.1-3mismatch_1_155_26 10.916622
CAL12325.1-4mismatch_1_19_62 10.812173
CAL12325.1-5mismatch_1_86_23 11.248517
CAL12325.1-6mismatch_1_112_96 10.61838
CAL12325.1-7mismatch_1_20_31 10.439825
CAL12325.1-8mismatch_1_119_26 10.281923
CAL12325.1-9mismatch_1_125_78 9.726209
CAL13917.1-15mismatch_1_68_85 8.406192
CAL13917.1-1mismatch_1_65_89 12.293757
CAL13917.1-2mismatch_1_13_9 12.257681
CAL13917.1-3mismatch_1_31_9 12.152917
CAL13917.1-4mismatch_1_38_67 12.033077
CAL13917.1-5mismatch_1_24_22 11.876898
CAL13917.1-6mismatch_1_147_90 11.517174
CAL13917.1-7mismatch_1_118_69 11.860309
CAL13917.1-8mismatch_1_95_51 11.810168
CAL13917.1-9mismatch_1_3_61 10.6987

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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