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Sample GSM1133916 Query DataSets for GSM1133916
Status Public on Nov 24, 2014
Title 100022_Macrophage_WNV
Sample type RNA
 
Source name Macrophage, severe disease, WNV
Organism Homo sapiens
Characteristics cell type: macrophages
treatment: West Nile virus (WNV)
age: 72
gender: male
batch: 1
phenotype: severe disease
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 6.589828711 0.4610389
ILMN_2055271 6.717339743 0.09220779
ILMN_1736007 6.642870992 0.2688312
ILMN_2383229 6.638842643 0.2818182
ILMN_1806310 6.572727536 0.5493507
ILMN_1779670 6.666344948 0.2064935
ILMN_1653355 6.714936471 0.09740259
ILMN_1717783 6.47525986 0.8948052
ILMN_1705025 6.680832081 0.1701299
ILMN_1814316 6.620572918 0.338961
ILMN_2359168 6.447571143 0.9324675
ILMN_1731507 6.390723042 0.9896104
ILMN_1787689 6.54600278 0.6597403
ILMN_3241953 7.903978702 0
ILMN_1745607 10.20887783 0
ILMN_2136495 6.373500814 0.9974026
ILMN_1668111 6.529016745 0.7246753
ILMN_2295559 6.837661238 0.01168831
ILMN_1735045 6.931283657 0.003896104
ILMN_1680754 6.683502692 0.1662338

Total number of rows: 47323

Table truncated, full table size 1548 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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