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Sample GSM988561 Query DataSets for GSM988561
Status Public on Oct 22, 2012
Title Healthy_SK96 [Illumina]
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics cell: PBMC
infection: Healthy
Extracted molecule total RNA
Extraction protocol Treatment-naïve HCV patients were recruited by hepatologists in the outpatient hepatitis clinic within the Yale Liver Center. Healthy volunteers were recruited from Yale’s PhenoGenetic Cohort of Healthy controls. PBMCs were isolated from whole blood by density gradient centrifugation using Ficoll-Paque (GE Healthcare) centrifugation. Total RNA was isolated from PBMCs using an RNeasy kit (Qiagen, Valencia, CA), and the quality of total RNA was evaluated by A260/A280 ratio and by electrophoresis on an Agilent Bioanalyzer.
Label biotin
Label protocol Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.
 
Hybridization protocol 1.5 µg of cRNA was combined with hybridization controls and hybridized to the array for 16 hours in a hybridization oven at 58°C. The chip was then washed and stained with streptavidin-Cy3.
Scan protocol The array was scanned using the Illumina BeadArray reader.
Description Human PBMC collected from whole blood of healthy volunteers
Data processing Microarray data from the validation cohort underwent quantile normalization using the Beadarray package in bioconductor.
 
Submission date Aug 20, 2012
Last update date Oct 22, 2012
Contact name Christopher Bolen
E-mail(s) [email protected]
Organization name Yale University
Department Pathology
Lab Steven Kleinstein
Street address 300 George Street, Suite 505
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL10558
Series (2)
GSE40223 The blood transcriptional signature of chronic HCV [Illumina data]
GSE40224 The blood transcriptional signature of chronic HCV

Data table header descriptions
ID_REF
VALUE BeadArray-normalized log2 signal values
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 6.765034755 0.5974026
ILMN_2055271 7.055673971 0.05324675
ILMN_1736007 6.828023477 0.3961039
ILMN_2383229 6.961879111 0.1194805
ILMN_1806310 6.836783828 0.3662338
ILMN_1779670 6.713789279 0.725974
ILMN_1653355 6.891029052 0.238961
ILMN_1717783 6.630413044 0.8896104
ILMN_1705025 7.115424503 0.03376623
ILMN_1814316 6.849456396 0.338961
ILMN_2359168 6.676577717 0.8
ILMN_1731507 6.667826856 0.8155844
ILMN_1787689 6.76743896 0.5922078
ILMN_3241953 7.872272254 0
ILMN_1745607 6.543194878 0.9896104
ILMN_2136495 6.622407396 0.9077922
ILMN_1668111 6.851110617 0.3298701
ILMN_2295559 6.816583068 0.4220779
ILMN_1735045 6.641567415 0.861039
ILMN_1680754 6.843678646 0.3519481

Total number of rows: 47323

Table truncated, full table size 1516 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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