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Sample GSM673246 Query DataSets for GSM673246
Status Public on Jun 17, 2011
Title Plasma_CS_rep4
Sample type RNA
 
Source name Cloudy Supernatant
Organism Homo sapiens
Characteristics tissue: plasma-derived
subfraction: cloudy supernatant
disease state: healthy
population: Caucasian
Treatment protocol All samples were initially spun at 1700g for 10 minutes to separate the plasma from the Buffy Coat and Red Blood Cells. Leukocytes were separately isolated from whole blood fractionated through Ficoll-Hypaque gradients. The plasma was re-centrifuged at 2000g for 10 minutes to obtain the Supernatant 1 (S1) and Pellet 1 (P1) fractions. The S1 fraction was additionally centrifuged at 12000g for 10 minutes to generate the Supernatant 2 (S2) and Pellet 2 (P2) fractions.
Growth protocol Blood was drawn in sodium EDTA tubes and processed within 4 hours of draw.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol-LS, Phenol:Chloroform and purified through Ambion mirVANA columns.
Label biotin
Label protocol A total of 500-1000ng of total RNA was labelled using the Genisphere HSR labelling Kit (http://www.genisphere.com/array_detection_flashtag_biotin.html).
 
Hybridization protocol The total amount of RNA was hybridized to the arrays for 16 hours at 48C with rotation at 60rpm.
Scan protocol Samples were scanned using the GCS 3000 7G Scanner and processed using miRNA_1-0_2xgain library files.
Description CS_4
miRNA expression data.
Data processing The data was preprocessed using the Affymetrix miRNA QC tool where Individual feature intensities were flagged by detection calls, background subtracted, transformed through addition of a small constant (value equal to 16) and median summarized. Non-normalized data was analyzed to preserve the individual distributions for rank correlation analysis.
 
Submission date Feb 10, 2011
Last update date Jun 17, 2011
Contact name Radha Duttagupta
E-mail(s) Radharani_Duttagupta@affymetrix.com
Phone 408-731-5691
Fax 408-731-5463
Organization name Affymetrix
Department Applied Research
Street address 3450 Central Expressway
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 
Platform ID GPL8786
Series (2)
GSE27230 Analysis of the impact of cellular miRNA signatures on the profiles of circulating miRNA biomarkers (fractionation data)
GSE27256 Impact of cellular miRNAs on the biomarker signatures of circulating miRNAs

Data table header descriptions
ID_REF
VALUE Background-subtracted, transformed, non-normalized data

Data table
ID_REF VALUE
14q-0_st 4.247927513
14qI-1_st 4.807354922
14qI-2_st 3.906890596
14qI-3_x_st 4.169925001
14qI-4_st 3.906890596
14qI-4_x_st 4.321928095
14qI-5_st 4.700439718
14qI-6_st 3.700439718
14qI-6_x_st 3.807354922
14qI-7_st 4.321928095
14qI-8_st 4.087462841
14qI-8_x_st 4.087462841
14qI-9_x_st 3.906890596
14qII-1_st 3.906890596
14qII-1_x_st 3.807354922
14qII-10_st 4.247927513
14qII-11_st 3.807354922
14qII-11_x_st 4
14qII-12_st 3.953445298
14qII-12_x_st 3.906890596

Total number of rows: 7752

Table truncated, full table size 207 Kbytes.




Supplementary file Size Download File type/resource
GSM673246.CEL.gz 160.0 Kb (ftp)(http) CEL
Processed data included within Sample table

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