|
| Status |
Public on May 11, 2015 |
| Title |
MARV PBMC, Mky 0705043 Day 9 |
| 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: 0705043
cell type: PBMC
time point (days post-infection): 9
|
| 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
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 |
Jun 06, 2014 |
| Last update date |
May 11, 2015 |
| Contact name |
Ignacio S. Caballero |
| E-mail(s) |
nacho@bu.edu
|
| Organization name |
Boston University School of Medicine
|
| Department |
NEIDL/Microbiology
|
| Street address |
620 Albany St., NEIDL 401V
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL10332 |
| Series (1) |
| GSE58287 |
Transcriptional Profiling of the Immune Response to Marburg Infection |
|
