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Sample GSM618009 Query DataSets for GSM618009
Status Public on Jan 12, 2011
Title AGS untreated rep 1
Sample type RNA
Source name AGS cells untreated for 8h rep 1
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 untreated AGS 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
VALUE log2 RMA signal

Data table
1007_s_at 11.093777
1053_at 10.496016
117_at 6.167629
121_at 8.686596
1255_g_at 3.981997
1294_at 5.666089
1316_at 6.176416
1320_at 7.624278
1405_i_at 4.119018
1431_at 4.536877
1438_at 6.362191
1487_at 9.755185
1494_f_at 5.902503
1552256_a_at 9.605232
1552257_a_at 9.421324
1552258_at 6.446914
1552261_at 6.458815
1552263_at 8.181082
1552264_a_at 8.802084
1552266_at 4.899318

Total number of rows: 54675

Table truncated, full table size 1057 Kbytes.

Supplementary file Size Download File type/resource
GSM618009.CEL.gz 5.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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