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Title: Toward a Better Understanding of Potential Roles of Astrocytes in HIV-1-associated Neurocognitive Disorders      
dateReleased:
08-05-2009
description:
We present a microarray analysis of primary mouse astrocytes exposed to HIV-1 in culture. Results are compared with previous genomic studies of HIV-1 effect in human astrocytes and human and macaque brains. Day-two neonatal mouse astrocytes were exposed in triplicates to cell-free HIV-1/NL4-3 at m.o.i. of 1 and cultured for 24 hours. As control, cells were treated in triplicates with a mock virus concentrate at the same dilution (vol/vol) as the wild-type virus. As an example of large scale gene expression analysis we shall provide some details of the method; full description is in Kim et al. (S.-Y. Kim et al., 2004). Total RNA was prepared from cell cultures using the RNAeasy total RNA extraction kit (Qiagen, CA). RNA quality was assessed by electrophoresis and spectrophotometric analysis; between 1 and 10 µg of total RNA was used to generate a cDNA, and then 1 µg of cDNA product was used in an in vitro transcription reaction that contained biotinylated UTP and CTP. Twenty µg of full-length cRNA was fragmented and was subjected to gene expression analysis on the Affymetrix Mouse Genome 430 2.0 Array chip. Affymetrix software was used to generate CHP files. Significance analysis was performed using ArrayAssist software (Stratagene).
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-17383
refinement:
raw
alternateIdentifiers:
17383
keywords:
functional genomics
dateModified:
03-27-2012
availability:
available
types:
gene expression
name:
Mus musculus
ID:
A-AFFY-45
name:
Affymetrix GeneChip Mouse Genome 430 2.0 [Mouse430_2]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-17383/E-GEOD-17383.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-17383/E-GEOD-17383.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17383
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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