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Sample GSM1023564 Query DataSets for GSM1023564
Status Public on Jun 18, 2013
Title LASV PBMC, Mky C38113 Day 10
Sample type RNA
 
Channel 1
Source name blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient
Organism Macaca fascicularis
Characteristics animal id: C38113
cell type: PBMC
time: Day 10 post-infection
infection: Lassa fever virus
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol reagent following the manufacturer's instructions
Label Cy5
Label protocol RNA samples were amplified and labeled with Cy dyes using the Agilent Low-Input Quick Amp Labeling kits
 
Channel 2
Source name Universal Human Reference RNA (Stratagene), commercially available
Organism Homo sapiens
Characteristics vendor: Agilent Technologies
catalog #: 740000
sample type: Universal Human Reference RNA (Stratagene)
rna source: 10 different human cell lines
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol reagent following the manufacturer's instructions
Label Cy3
Label protocol RNA samples were amplified and labeled with Cy dyes using the Agilent Low-Input Quick Amp Labeling kits
 
 
Hybridization protocol Labeled reference RNA was added to each experimental sample, then samples were hybridized to arrays in Agilent SureHyb-enabled hybridization chambers. After a 17-hour hybridization, arrays were washed with the Agilent gene expression wash buffers and then placed in Agilent scanner slide holders with ozone-barrier covers.
Scan protocol Arrays were scanned using the Agilent High-Resolution Microarray Scanner and raw microarray images were processed using Agilent's Feature Extraction software
Description commercially available human reference RNA from Agilent (Stratagene), used as a consistent control in dataset comparisons
Data processing Data were first background-corrected to remove noise from background intensity levels, and then normalized within the arrays using the Limma package in R (R development core team 2010). Following normalization, the reference and experimental samples were compared to generate log fold-change values that represent a change in mRNA expression (either positive or negative). Data were further processed by zero-transformation, where the normalized values of the pre-infection samples were subtracted from the subsequent timepoints of each monkey, in order to remove animal-intrinsic variables and focus on gene expression changes due to infection only.
 
Submission date Oct 22, 2012
Last update date Jun 18, 2013
Contact name Judy Yen
E-mail(s) jyen@bu.edu
Phone 617-414-8918
Organization name Boston University School of Medicine
Department NEIDL/Microbiology
Street address 620 Albany St., Rm 401H
City Boston
State/province MA
ZIP/Postal code 02118
Country USA
 
Platform ID GPL4133
Series (1)
GSE41752 Transcriptional Profiling in Non-Human Primates Infected With Lassa Virus to Understand the Immune Response to Lassa Infection

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (test/reference) of samples, before zero-transformation

Data table
ID_REF VALUE
1 0.664807014
2 -0.152865052
3 -0.141878018
4 -0.032468966
5 -0.039260988
6 -0.073945755
7 -0.080586833
8 -0.054257818
9 -0.089800057
10 0.022150792
11 -0.084991981
12 3.24591001
13 -0.042661049
14 0.235944574
15 -0.259259524
16 -0.355709573
17 -0.689521651
18 0.831461023
19 0.018568865
20 0.121528479

Total number of rows: 45015

Table truncated, full table size 797 Kbytes.




Supplementary file Size Download File type/resource
GSM1023564_US22502646_251485030204_S01_GE2-v5_95_Feb07_1_4.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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