Comment[ArrayExpressAccession]	E-GEOD-54385
MAGE-TAB Version	1.1						
Public Release Date	2014-04-22
Investigation Title	A comparison of gene expression between human dermal fibroblasts and neurons infected by varicella zoster virus						
Comment[Submitted Name]	A comparison of gene expression between human dermal fibroblasts and neurons infected by varicella zoster virus
Experiment Description	The cellular transcriptomes of VZV-infected fibroblasts and T-lymphocytes have been reported, but not that of human neurons. In order to determine the transcriptional response of human neurons to VZV infection, we generated 95%-pure populations of neurons from hESC, infected them with recombinant GFP-expressing cell-free VZV, and compared their transcriptome to that of human foreskin fibroblasts infected in parallel, using Agilent microarrays.  Applying a twofold-change as the cutoff (p-value<0.05), we observed that transcription of 1654 fibroblast and 340 neuronal genes were upregulated, and 955 fibroblast and 38 neuronal genes were downregulated by VZV infection. 223 of these infection-regulated genes were unique to neurons. Gene ontology enrichment analysis revealed several clusters of genes regulated by VZV in neurons and fibroblasts differed. For example, neurons did not show upregulation of innate immune responses, NF-kappaB, response to stress and DNA repair clusters, in contrast to fibroblasts that upregulated these groups. This is the first study of the response of genetically normal human neurons to viral infection. Two-condition experiment, VZV-GFP23- fibroblast cells vs. fibroblast cells, and VZV-GFP23- neuron cells vs. neuron cells. Data from two biological replicates and two technical replicates were used for each condition.						
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	Waldman Ben-Asher	Markus	Waldman Ben-Asher	Kinchington	Goldstein		
Person First Name	Hiba	Amos	Hiba	Paul	Ronald		
Person Mid Initials				R	S		
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	Bar-Ilan University						
Person Address	Life-Sciences, Bar-Ilan University, Ramat-Gan, Ramat-Gan, Israel						
Person Roles	submitter						
Protocol Name	P-GSE54385-1	P-GSE54385-5	P-GSE54385-6	P-GSE54385-2	P-GSE54385-3	P-GSE54385-4	P-GSE54385-7
Protocol Description	The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (version 9.5.1.1 Agilent Technologies, Santa Clara, CA). The rest of the analysis was performed in Partek® Genomics Suite software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.The log expression ratios that were produced during the normalization step were analyzed. ID_REF =  VALUE = Normalized log2 ratio (Cy5/Cy3)	200 ng of total RNA, in the presence of control RNAs (RNA spike-in kit; Agilent), for each sample was labeled with either Cy-3 or Cy-5 using the Low Input Quick Amp Labeling Kit, two-color (Agilent) following the manufacturer's protocol.	Equal amounts of labeled RNA were then hybridized on the chip, per the Agilent protocol, at 60 degrees overnight. The hybridization mixes were prepared using the Gene Expression Hybridization Kit from Agilent following the manufacturer's protocol. After hybridization, the slide was washed first with Gene Expression Wash Buffer 1 (Agilent) and then Gene Expression Wash Buffer 2 (Agilent). This was followed by an acetonitrile wash and finally the slides were placed in Stabilization & Drying Solution (Agilent). The washed slides were scanned on an Agilent G2565BA scanner. Feature extraction was performed using the Feature Extraction software from Agilent.	GFP fluorescence was used to determine infection. Cells were harvested for RNA extraction when 80% of the neurons and over 90% of the fibroblasts expressed GFP.	The fibroblasts are primary cells obtained from a single biopsy. Fibroblasts were grown according to standard protocol. hESC-derived (line H9) neurons were generated by PA6 induction as described in Grigoryan S et al. J. Neurovirol. 2012.	Total RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit (sigma) according to the manual protocol.	Scanned on an Agilent G2565BA microarray scanner.
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	TREATMENT	CELL TYPE	INFECTION DAY				
Experimental Factor Type	treatment	cell type	infection day				
Publication Title	Cellular transcriptome analysis reveals differential expression of pro- and anti-apoptosis genes by Varicella zoster virus-infected neurons and fibroblasts.						
Publication Author List	Markus A, Waldman Ben-Asher H, Kinchington PR, Goldstein RS						
PubMed ID	24741086						
Publication DOI	10.1128/JVI.00500-14						
Comment[SecondaryAccession]	GSE54385						
Comment[GEOReleaseDate]	2014-04-22						
Comment[ArrayExpressSubmissionDate]	2014-01-24						
Comment[GEOLastUpdateDate]	2014-04-22						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-54385.sdrf.txt