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Title: Effect of p38 MAPK inhibitor SB203580 on gene expression in monocytic THP-1 cells stimulated with HIV gp120 or LPS      
dateReleased:
12-25-2014
description:
Human monocytic THP-1 cells were exposed to HIV envelope protein gp120 or bacterial LPS in the presence and absence of a pharmacological inhibitor of the p38 mitogen-activated protein kinase (MAPK) for 4 and 24 hours. A microarray analysis was performed in order to assess differential gene expression at the RNA level. Human monocytic THP-1 cells were pre-treated for 15 min with 10 µM SB203580 followed by exposure for 4 h or 24 h to 1 nM HIV gp120SF162 or 1 µg/ml LPS. 0.1 % DMSO and 0.001 % BSA served as vehicle controls for SB203580 and gp120, respectively. The experimental samples were 1) control 4 h, 2) gp120 4 h, 3) LPS 4 h, 4) SB203580 (SB) 4 h, 5) SB+gp120 4 h, 6) SB+LPS 4 h, 7) control 24 h, 8) gp120 24 h, 9) LPS 24 h, 10) SB 24 h, 11) SB+gp120 24 h, 12) SB+LPS 24 h. RNA was isolated from three biological replicates for each experimental condition using an RNeasy kit commercially available from Qiagen (Valencia, CA). Roughly 2 X 106 cells were collected to obtain 500 ng – 2 µg RNA. RNA quality (A260/A280 ratio ~1.8-2.0) was tested using the NanoDrop system from Thermo Scientific (Rockford, IL). High quality RNA was then provided to the Microarray/ QPCR Facility Core at Sanford-Burnham Medical Research Institute and DNA microarray was performed using the whole genome gene-expression analysis HumanHT-12 v4 Expression BeadChip kit from Illumina (San Diego, CA). Microarray results were further analyzed by Dr. Roy Williams (Bioinformatics Core, Sanford-Burnham Medical Research Institute) using the GeneSpring GX platform
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-53712
refinement:
raw
alternateIdentifiers:
53712
keywords:
functional genomics
dateModified:
01-02-2015
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-GEOD-10558
name:
Illumina HumanHT-12 V4.0 expression beadchip
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-53712/E-GEOD-53712.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-53712/E-GEOD-53712.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=GSE53712
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