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Sample GSM224705 Query DataSets for GSM224705
Status Public on Feb 05, 2016
Title Caco-2 EAV9-2
Sample type RNA
 
Source name 2 h with 1x10E8 S. enteritidis strain EAV9
Organism Homo sapiens
Characteristics Caco-2: human, Caucasian, colon, adenocarcinoma
Biomaterial provider ECACC
Treatment protocol Caco-2 cells were grown in 100-mm culture dishes to 3 days post-confluence in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics. Cells were washed twice with HBSS (Sigma) and incubated for 24 h in DTS medium containing DMEM, L-glutamine, transferrin and sodium selenite before incubation for 2 h with 1x10E8 S. enteritidis strain EAV9.
Growth protocol Caco-2 cells were grown in culture flasks in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted with an RNeasy kit (Qiagen) and included a DNAse I step (Qiagen). Poly (A)+ RNA was purified using an Oligotex mRNA mini kit (Qiagen).
Label Biotin
Label protocol Fragmented and biotin-labelled cRNA was synthesized from 1 ug purified mRNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.
Description Caco-2 cells were treated with Salmonella enteritidis strains S1400 or EAV9 or recombinant flagellin, and their gene expression profile was compared to non-stimulated cells.
Data processing Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA, p-values were adjusted using the Benjamini-Hochberg method.
 
Submission date Aug 24, 2007
Last update date Aug 28, 2018
Contact name Denise Kelly
E-mail(s) D.Kelly@rri.sari.ac.uk
Phone +44 1224 716648
Organization name University of Aberdeen
Lab Gut Immunology Group
Street address Institute of Medical Sciences
City Aberdeen
ZIP/Postal code AB25 2ZD
Country United Kingdom
 
Platform ID GPL570
Series (1)
GSE8896 Flagellin-mediated effects of Salmonella enteritidis on gene expression in intestinal epithelial cells
Relations
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE gcRMA normalized signal intensity, log2 scaled

Data table
ID_REF VALUE
1007_s_at 11.41556381
1053_at 8.841406134
117_at 2.49579122
121_at 6.330621354
1255_g_at 2.266377596
1294_at 2.053764715
1316_at 2.965619807
1320_at 7.076226139
1405_i_at 3.655646123
1431_at 2.763983781
1438_at 2.228545891
1487_at 10.02752189
1494_f_at 2.625517679
1552256_a_at 12.09326575
1552257_a_at 9.920655298
1552258_at 2.335817854
1552261_at 2.706152359
1552263_at 7.422088437
1552264_a_at 9.107642278
1552266_at 2.86644686

Total number of rows: 54675

Table truncated, full table size 1035 Kbytes.




Supplementary file Size Download File type/resource
GSM224705.CEL.gz 5.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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