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Sample GSM618012 Query DataSets for GSM618012
Status Public on Jan 12, 2011
Title AGS treated rep 2
Sample type RNA
 
Source name AGS cells treated with 10 μg/ml H. pylori LPS for 8h rep 2
Organism Homo sapiens
Characteristics cell type: gastric epithelial cells
cell line: AGS
Treatment protocol The morning of treatment, the cell culture medium was replaced with either fresh medium (untreated) or medium containing 10 μg/ml H. pylori lipopolysaccharide
Growth protocol AGS cells were routinely maintained in nutrient mixture F-12 Ham (Sigma) supplemented with 10% foetal calf serum (Gibco), 2 mM L-glutamine (Sigma), 100 U/ml penicillin (Sigma) and 100 μg/ml streptomycin. The day before treatment, cells were seeded in 6-well plates at 1x106 cells/well.
Extracted molecule total RNA
Extraction protocol 8h post-stimulation, cells were harvested and RNA isolated using the Nucleospin RNAII kit (Machery Nagel) according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) using the Affymetrix IVT labeling kit.
 
Hybridization protocol Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 genechips. GeneChips were washed and stained in the Automated fluidics 450 station.
Scan protocol Genechips were scanned using the GeneChip 3000 7G scanner
Description gene expression in H. pylori LPS-treated cells
Data processing Scanned images, obtained using Affymetrix Software (MAS5), were normalized using robust multichip average (RMA) analysis with RMAExpress version 0.4.1.
 
Submission date Nov 04, 2010
Last update date Jan 13, 2011
Contact name Sinead Marian Smith
Organization name Trinity College Dublin
Lab Trinity Centre for Health Sciences
Street address St. James's Hospital
City Dublin 8
ZIP/Postal code D8
Country Ireland
 
Platform ID GPL570
Series (2)
GSE25146 Changes in gene expression in AGS cells in response to Helicobacter pylori lipopolysaccharide
GSE25155 Tribbles 3 - a novel regulator of TLR2-mediated signaling in response to Helicobacter pylori lipopolysaccharide

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
1007_s_at 11.262687
1053_at 10.479567
117_at 6.302742
121_at 8.9005
1255_g_at 4.059374
1294_at 5.966315
1316_at 6.346382
1320_at 7.59804
1405_i_at 4.180656
1431_at 4.491995
1438_at 6.563031
1487_at 9.996295
1494_f_at 6.033183
1552256_a_at 9.965304
1552257_a_at 9.701941
1552258_at 6.362264
1552261_at 6.35618
1552263_at 7.78542
1552264_a_at 8.801276
1552266_at 5.068708

Total number of rows: 54675

Table truncated, full table size 1057 Kbytes.




Supplementary file Size Download File type/resource
GSM618012.CEL.gz 5.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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