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Sample GSM1133946 Query DataSets for GSM1133946
Status Public on Nov 24, 2014
Title 110483_PBMC_WNV
Sample type RNA
 
Source name PBMC, asymptomatic, WNV
Organism Homo sapiens
Characteristics cell type: peripheral blood mononuclear cells (PBMCs)
treatment: West Nile virus (WNV)
age: 55
gender: female
batch: 2
phenotype: asymptomatic
Extracted molecule total RNA
Extraction protocol Total RNA from PBMC and macrophage samples was extracted using the RNeasy mini kit (Qiagen, CA).
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 Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip. The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours. After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.
Scan protocol The BeadChips were scanned on the Illumina Iscan.
Data processing The data were normalised using quantile normalisation with lumi in R.
 
Submission date May 06, 2013
Last update date Nov 24, 2014
Contact name Hailong Meng
Organization name Yale University
Street address 300 George Str
City New Haven
State/province CT
ZIP/Postal code 06525
Country USA
 
Platform ID GPL10558
Series (1)
GSE46681 Profiling the successful response to infection with West Nile virus

Data table header descriptions
ID_REF
VALUE Quantile and then log2 normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 6.617953319 0.2883117
ILMN_2055271 6.645079571 0.2194805
ILMN_1736007 6.670144781 0.1571429
ILMN_2383229 6.594235139 0.3844156
ILMN_1806310 6.593883731 0.387013
ILMN_1779670 6.685365084 0.1155844
ILMN_1653355 6.659936439 0.1831169
ILMN_1717783 6.480751796 0.8467532
ILMN_1705025 6.625528009 0.2636364
ILMN_1814316 6.635353231 0.2428571
ILMN_2359168 6.43804492 0.9350649
ILMN_1731507 6.468932004 0.8779221
ILMN_1787689 6.61464546 0.2987013
ILMN_3241953 6.978130241 0
ILMN_1745607 6.738944072 0.03246753
ILMN_2136495 6.380207289 0.9844156
ILMN_1668111 6.542635073 0.6168831
ILMN_2295559 6.599881787 0.3571429
ILMN_1735045 7.016979167 0
ILMN_1680754 6.556382148 0.5519481

Total number of rows: 47323

Table truncated, full table size 1493 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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