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Sample GSM764044 Query DataSets for GSM764044
Status Public on Jul 20, 2011
Title Patient nucleic acid sample BMA_HPA_038
Sample type other
Source name Patient 4 Cerebrospinal fluid Sample
Organism Homo sapiens
Characteristics extracted molecule: total nucleic acids
cell/tissue type: cerebrospinal fluid
Treatment protocol CSF samples were centrifuged for 5 minutes at 1000 g to remove cellular debris, 200 ul aliquots of the supernatant fraction were then removed and centrifuged at 13000 g for 10 minutes. The pellet and supernatant fractions were recovered and processed separately. The pellet fraction was re-suspended in 200 ul of TBE buffer prior to further processing.
Growth protocol N/A
Extracted molecule other
Extraction protocol
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
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
VALUE Bluefuse™ analysis software-computed normalised to global median using Cy3 signal intensity, replicate data points fused on median and name.

Data table
1145789-1-A01Foot-and-mouthdiseasevirusO 11.626
1145789-1-A02Foot-and-mouthdiseasevirusO 85.072
1145789-1-A03Alcelaphineherpesvirus1 16.698
1145789-1-A04Alcelaphineherpesvirus1 49.415
1145789-1-A05Acutebeeparalysisvirus 1042.205
1145789-1-A06Acutebeeparalysisvirus 12.601
1145789-1-A07Gallidherpesvirus3 28.245
1145789-1-A08Humanparainfluenzavirus3 23.663
1145789-1-A09Humanparainfluenzavirus3 22.55
1145789-1-A10Echovirus5 26.681
1145789-1-A11Lelystadvirus 104.017
1145789-1-A12NewcastlediseasevirusB1 2164.009
1145789-1-B01Foot-and-mouthdiseasevirusO 21.84
1145789-1-B02Foot-and-mouthdiseasevirusO 63.235
1145789-1-B03Alcelaphineherpesvirus1 41.709
1145789-1-B04Lactatedehydrogenase-elevatingvirus 104.517
1145789-1-B05Acutebeeparalysisvirus 105.084
1145789-1-B06Gallidherpesvirus3 69.761
1145789-1-B07Gallidherpesvirus3 181.009
1145789-1-B08Humanparainfluenzavirus3 156.835

Total number of rows: 2177

Table truncated, full table size 70 Kbytes.

Supplementary file Size Download File type/resource
GSM764044_CSF4_Supernatant.txt.gz 667.9 Kb (ftp)(http) TXT
GSM764044_CSF4_Supernatant_Normalised.txt.gz 140.5 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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