|
Status |
Public on Jun 18, 2013 |
Title |
LASV PBMC, Mky C38113 Day -8 |
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 -8 pre-infection infection: pre-infection
|
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
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|
|
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
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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.
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|
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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 |
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