Comment[ArrayExpressAccession]	E-GEOD-49838
MAGE-TAB Version	1.1						
Public Release Date	2014-08-29
Investigation Title	Transcriptional comparison of cynomolgus macaques (Macaca fascicularis) following infection with Lassa or Lujo viruses						
Comment[Submitted Name]	Transcriptional comparison of cynomolgus macaques (Macaca fascicularis) following infection with Lassa or Lujo viruses
Experiment Description	Microarray analysis of PBMC from cynomolgus macaques collected longitudinally over the course of infection with Lassa-Josiah, Lassa-Z132, Lassa-SorombaR, or Lujo viruses (n=3 animals/infection condition). 3 macaques from each group were infected intramuscularly with 10^4 PFU of Lassa-Josiah, Lassa-Z132, Lassa-SorombaR, or Lujo viruses.  PBMC were collected at days 1, 4, 7, 10, 13, and 29 (for surviving animals).  We performed microarray analysis on PBMC samples using Agilent rhesus macaque arrays on all samples, as well as on PBMC from 3 uninfected animals for use as a control.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Katze	Rasmussen	Tchitchek	Katze	Safronetz	Feldmann	
Person First Name	Michael	Angela	Nicolas	Michael	David	Heinrich	
Person Email	data@viromics.washington.edu						
Person Affiliation	University of Washington						
Person Address	Microbiology, University of Washington, Rosen Building 960 Republican St., Seattle, WA, USA						
Person Roles	submitter						
Protocol Name	P-GSE49838-1	P-GSE49838-5	P-GSE49838-6	P-GSE49838-2	P-GSE49838-3	P-GSE49838-4	P-GSE49838-7
Protocol Description	Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the using the M-bM-^@M-^XnormalizeBetweenArraysM-bM-^@M-^Y normalization method available in the M-bM-^@M-^XlimmaM-bM-^@M-^Y package of the R suite. ID_REF =  VALUE = normalized signal	The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.	The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K rhesus macaque array.	PBMC were isolated by Ficoll density gradient centrifugation, washed in PBS, preserved in 0.5 mL AVL buffer diluted 1:1 with 70% ethanol, and stored at -80M-:C prior to further processing.	3 adult cynomolgus macaques (Macaca fascicularis) aged 3-7 years were infected under anesthesia with 10e4 PFU LASV or LUJV by intramuscular inoculation. PBMC were collected on days 1, 4, 7, 10, 13 and 29 (for surviving LUJV-infected animals) post-infection. Additionally, PBMC were collected from 3 uninfected animals for use as a control.	Samples were thawed and diluted with 2 volumes RLT buffer, and then adjusted to a 1:1 ratio with 70% ethanol. All extractions were performed using Qiagen RNeasy Micro columns with the manufacturer's recommended protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer using the picochip format, and only intact RNA was used for microarray analyses.	Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TIME	INFECTION					
Experimental Factor Type	time	infection					
Comment[SecondaryAccession]	GSE49838						
Comment[GEOReleaseDate]	2014-08-29						
Comment[ArrayExpressSubmissionDate]	2013-08-13						
Comment[GEOLastUpdateDate]	2014-08-29						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-49838.sdrf.txt