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Sample GSM618015 Query DataSets for GSM618015
Status Public on Jan 12, 2011
Title MKN45 treated rep 1
Sample type RNA
 
Source name MKN45 cells treated with 10 μg/ml H. pylori LPS for 8h rep 1
Organism Homo sapiens
Characteristics cell type: gastric epithelial cells
cell line: MKN45
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 MKN45 cells were routinely maintained in RPMI (Gibco) 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)
GSE25147 Changes in gene expression in MKN45 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 12.35919
1053_at 10.645739
117_at 7.142258
121_at 9.568179
1255_g_at 4.327966
1294_at 6.845467
1316_at 7.348688
1320_at 6.882848
1405_i_at 4.310133
1431_at 5.78115
1438_at 7.663968
1487_at 10.19715
1494_f_at 7.355492
1552256_a_at 10.740668
1552257_a_at 10.478794
1552258_at 7.000974
1552261_at 7.183917
1552263_at 6.882855
1552264_a_at 8.357196
1552266_at 5.565103

Total number of rows: 54675

Table truncated, full table size 1058 Kbytes.




Supplementary file Size Download File type/resource
GSM618015.CEL.gz 5.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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