Comment[ArrayExpressAccession]	E-GEOD-11195
Public Release Date	2008-04-18
Investigation Title	Detection of Human Viruses from wastewater sewage extracts									
Comment[Submitted Name]	Detection of Human Viruses from wastewater sewage extracts
Experiment Description	Sewage samples were collected and concentrated for Human and animal viruses. Viruses were cultured on Buffalo Green Monkey Cells (BGMK) and their genomic DNA/RNA were extracted and labeled with Cy3 and Cy5 respectively. Labeled DNA/RNA were hybridized unto the array and signals generated were analyzed to indicate the presence of target viruses. Keywords: Detection of pathogens within environmental sample (Viruses) Environmental viruses were concentrated using organic flocculation with Beef Extract supplemented with glycine. Viruses were concentrated using 2 successive rounds of centrifugation and resuspended in Sodium Phosphate buffer. Viral nucleic acid was extracted, labeled and hybridized unto the microarray to determine the presence of target viruses within the sample.									
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Term Source Name	EFO
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Term Source File	http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/efo.owl									
Person Last Name	Wong	Wong	Rose							
Person First Name	Mark	Mark	Joan							
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Person Email	geo@ncbi.nlm.nih.gov									
Person Affiliation	Rose_Lab@MSU									
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Person Address	Crops and Soil Sciences, Rose_Lab@MSU, 3 Natural Resources, East Lansing, MI, USA									
Person Roles	submitter									
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Protocol Name	P-GSE11195-1	P-GSE11195-8	P-GSE11195-3	P-GSE11195-10	P-GSE11195-9	P-GSE11195-2	P-GSE11195-4	P-GSE11195-6	P-GSE11195-7	P-GSE11195-5
Protocol Description	ID_REF = <br>VALUE = Signal value<br>Cy3_signal = Cy3 Signal<br>Cy5_signal = Cy5 Signal<br>Cy3_Median = Cy3 Median value, same as signal<br>Cy3_Mean = Cy3 Mean<br>Cy3_SD = Cy3 standard deviation<br>Cy5_Median = Cy5 Median value, same as signal<br>Cy5_Mean = Cy5 Mean<br>Cy5_SD = Cy5 standard devaition<br>FLAG = Flag value. Null if empty spot<br>PRE_VALUE = Cy3 / Cy5 value, flagged	Hybridization was carried out in 50 ul hybridization buffer at 20 degrees Celsius using a microfluidic hybridization wash station. Hybridization was allowed to proceed for at least 17 hours before washing and scanning.	Buffalo Green Monkey cells were coated with 12 ml virus concentrate and allowed to contact for 2 hrs with occassional rocking.	Signal values were derived from the RAW data files by extracting the median foreground intensity for each given spot.	Arrays were scanned in a Genepix 4000B microarray scanner at PMT values of appoximately 700.	Virus was concentrated through organic flocculation with 15% Beef extract supplemented with glycine and concentrated by centrifugation. Viruses were resuspended in Sodium phosphate buffer and stored prior to cell culture	Viral DNA extracted using QIAGEN viral RNA extraction kit following manufacturer's protocol.	Viral RNA extracted using QIAGEN viral RNA extraction kit following manufacturer's protocol.	Total RNA was labeled with Cy5 using Sensicript III reverse transcriptase and random hexamer primers. Cyanine dye was indirectly coupled via amino allyl-dUTP.	Total nucleic acid extract was treated with DPN II restriction enzyme for 1 hr. Labeled with Cy3 using Klenow fragment and random hexamer primers. Cyanine dye was indirectly coupled via amino allyl-dUTP.
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Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	nucleic_acid_extraction	labeling	labeling
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Comment[SecondaryAccession]	GSE11195									
Comment[GEOLastUpdateDate]	2009-03-15
Comment[AEExperimentType]	other									
Comment[GEOReleaseDate]	2008-04-17
Comment[ArrayExpressSubmissionDate]	2008-04-15
SDRF File	E-GEOD-11195.sdrf.txt