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Sample GSM1058082 Query DataSets for GSM1058082
Status Public on Dec 29, 2012
Title PBMC_Severe_Disease 7
Sample type RNA
 
Source name PBMC, severe disease, mock
Organism Homo sapiens
Characteristics cell type: peripheral blood mononuclear cells (PBMCs)
treatment: mock
age: 49
gender: Male
batch: 2
disease status: Severe Disease
disease severity/outcome: Encephalitis
Extracted molecule total RNA
Extraction protocol Total RNA from PBMC 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 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. The BeadChips were scanned on the Illumina Iscan.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Severe Disease
Data processing The data were normalised using quantile normalisation with lumi (lumi_2.4.0) in R version 2.13.2 (2011-09-30)
 
Submission date Dec 28, 2012
Last update date May 06, 2013
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 (2)
GSE43190 Serum predictors of susceptibility to infection with West Nile virus
GSE46681 Profiling the successful response to infection with West Nile virus

Data table header descriptions
ID_REF
VALUE quantile and then log2 normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 6.651589284 0.1636364
ILMN_2055271 6.776112277 0.01038961
ILMN_1736007 6.551572212 0.5935065
ILMN_2383229 6.56867307 0.5064935
ILMN_1806310 6.651071473 0.1636364
ILMN_1779670 6.512336975 0.7584416
ILMN_1653355 6.651820845 0.1636364
ILMN_1717783 6.466607383 0.8961039
ILMN_1705025 6.571521328 0.4896104
ILMN_1814316 6.544842324 0.6298701
ILMN_2359168 6.435402055 0.9610389
ILMN_1731507 6.426226391 0.974026
ILMN_1787689 6.532710342 0.6805195
ILMN_3241953 7.224515707 0
ILMN_1745607 9.02061474 0
ILMN_2136495 6.437183427 0.9558442
ILMN_1668111 6.544300092 0.6311688
ILMN_2295559 6.582630406 0.4285714
ILMN_1735045 6.739416289 0.01428571
ILMN_1680754 6.501886303 0.7818182

Total number of rows: 47323

Table truncated, full table size 1498 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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