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Sample GSM764069 Query DataSets for GSM764069
Status Public on Jul 20, 2011
Title No DNA Control sample BMA_HPA_063
Sample type other
 
Source name Buffer only control
Organism Homo sapiens
Characteristics extracted molecule: None
cell/tissue type: Buffer only control
Treatment protocol N/A
Growth protocol N/A
Extracted molecule other
Extraction protocol http://www.qiagen.com/products/genomicdnastabilizationpurification/qiaampsystem/qiaampdnaminikit.aspx
Label Cy3
Label protocol The method used to generate randomly amplified DNA targets is a modification of the method published by Bohlander et al and has been described previously (see references 1 and 2 below)
Reference 1: Bohlander SK, Espinosa R 3rd, Le Beau MM, Rowley JD, Diaz MO. 1992 A method for the rapid sequence-independent amplification of microdissected chromosomal material. Genomics. 13:1322-4.
Reference 2: Burton, J. E., O. J. Oshota, E. North, M. J. Hudson, N. Polyanskaya, J. Brehm, G. Lloyd, and N. J. Silman. 2005. Development of a multi-pathogen oligonucleotide microarray for detection of Bacillus anthracis. Mol Cell Probes 19:349-57
 
Hybridization protocol Slides were pre-hybridised in 5 x SSC, 0.1% SDS and 4 x Denhardts solution, washed in sterile, nuclease-free water followed by 100% propan-2-ol then air-dried. Cy3-labelled randomly-amplified target DNAs were denatured at 95 oC for 3 minutes then diluted to a final concentration of 80 μg/ml in 5 x SSC buffer (Sigma-Aldrich), 0.1% SDS, 4 x Denhardts solution at 50oC. 40 μl of hybridisation mix was applied to the microarray slide, which was then incubated in a humidified multi-slide chamber (Genetix Inc.) for 16 hours. The slides were then washed once in each of the following buffers for two minutes: (A) 1 x SSC, 0.2% SDS, 50oC, (B) 0.1 x SSC, 0.2% SDS, 50oC, (C) 0.1 x SSC, 0.2% SDS, 20oC, then centrifuged to dryness at 1000 rpm for 5 minutes
Scan protocol scanned using an Affymetrix 428 microarray laser scanner at a gain of sixty
Data processing After image capture files were saved in Tiff format then quantified using the scan analysis software Bluefuse™ (BlueGnome Inc. Cambridge UK), all data were normalised to the global median for each slide then replicate data points fused according to median fluorescent intensity and name. The data were sorted into pathogen relevant groups and each group analysed for statistical significance. Probe intensities were derived for each sample, the log(2) taken and p values calculated which were then sorted from lowest to highest values within each group. Data points for each group were then ranked first by decreasing fold intensity over human DNA control hybridisation values and then by significance (only oligonucleotides with p < 0.2 in each group were considered).
 
Submission date Jul 19, 2011
Last update date Jul 20, 2011
Contact name Karen Elizabeth Kempsell
E-mail(s) karen.kempsell@ukhsa.gov.uk
Phone ++44(0)1980 619816
Organization name UK Health Security Agency
Department Science Group
Lab Diagnostic Technologies
Street address Porton Down
City Salisbury
State/province Wiltshire
ZIP/Postal code SP4 0JG
Country United Kingdom
 
Platform ID GPL13948
Series (1)
GSE30794 Design of a Diagnostic Pan-Pathogen Oligonucleotide Microarray including a sub-Array for Detection of Meningitis-Causing Bacterial Pathogens

Data table header descriptions
ID_REF
VALUE Bluefuse™ analysis software-computed normalised to global median using Cy3 signal intensity, replicate data points fused on median and name.

Data table
ID_REF VALUE
1145789-1-A01Foot-and-mouthdiseasevirusO 1037.942
1145789-1-A02Foot-and-mouthdiseasevirusO 761.859
1145789-1-A03Alcelaphineherpesvirus1 824.339
1145789-1-A04Alcelaphineherpesvirus1 1176.161
1145789-1-A05Acutebeeparalysisvirus 1180.813
1145789-1-A06Acutebeeparalysisvirus 1551.277
1145789-1-A07Gallidherpesvirus3 1176.648
1145789-1-A08Humanparainfluenzavirus3 888.972
1145789-1-A09Humanparainfluenzavirus3 501.8
1145789-1-A10Echovirus5 278.891
1145789-1-A11Lelystadvirus 556.688
1145789-1-A12NewcastlediseasevirusB1 703.068
1145789-1-B01Foot-and-mouthdiseasevirusO 180.046
1145789-1-B02Foot-and-mouthdiseasevirusO 739.189
1145789-1-B03Alcelaphineherpesvirus1 886.325
1145789-1-B04Lactatedehydrogenase-elevatingvirus 514.095
1145789-1-B05Acutebeeparalysisvirus 1164.707
1145789-1-B06Gallidherpesvirus3 1050.701
1145789-1-B07Gallidherpesvirus3 1006.442
1145789-1-B08Humanparainfluenzavirus3 1261.966

Total number of rows: 2177

Table truncated, full table size 69 Kbytes.




Supplementary file Size Download File type/resource
GSM764069_No_DNA_Control_F.txt.gz 651.1 Kb (ftp)(http) TXT
GSM764069_No_DNA_Control_Normalised_F.txt.gz 132.5 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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