GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM764048 Query DataSets for GSM764048
Status Public on Jul 20, 2011
Title Patient nucleic acid sample BMA_HPA_042
Sample type other
Source name Patient 6 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 60.771
1145789-1-A02Foot-and-mouthdiseasevirusO 91.737
1145789-1-A03Alcelaphineherpesvirus1 163.096
1145789-1-A04Alcelaphineherpesvirus1 100.888
1145789-1-A05Acutebeeparalysisvirus 1923.816
1145789-1-A06Acutebeeparalysisvirus 157.95
1145789-1-A07Gallidherpesvirus3 78.985
1145789-1-A08Humanparainfluenzavirus3 85.786
1145789-1-A09Humanparainfluenzavirus3 76.439
1145789-1-A10Echovirus5 196.965
1145789-1-A11Lelystadvirus 120.994
1145789-1-A12NewcastlediseasevirusB1 1601.99
1145789-1-B01Foot-and-mouthdiseasevirusO 590.471
1145789-1-B02Foot-and-mouthdiseasevirusO 107.174
1145789-1-B03Alcelaphineherpesvirus1 515.287
1145789-1-B04Lactatedehydrogenase-elevatingvirus 606
1145789-1-B05Acutebeeparalysisvirus 3149.319
1145789-1-B06Gallidherpesvirus3 459.586
1145789-1-B07Gallidherpesvirus3 7920.547
1145789-1-B08Humanparainfluenzavirus3 193.128

Total number of rows: 2177

Table truncated, full table size 69 Kbytes.

Supplementary file Size Download File type/resource
GSM764048_CSF6_Supernatant.txt.gz 666.5 Kb (ftp)(http) TXT
GSM764048_CSF6_Supernatant_Normalised.txt.gz 139.5 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap