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Sample GSM224701 Query DataSets for GSM224701
Status Public on Feb 05, 2016
Title Caco-2 S1400-2
Sample type RNA
 
Source name 2 h with 1x10E8 S. enteritidis strain S1400
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 S1400.
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 11.66893527
1053_at 8.796904873
117_at 2.483080576
121_at 6.31933928
1255_g_at 2.264578641
1294_at 2.052479908
1316_at 2.963602056
1320_at 6.913501506
1405_i_at 3.57784195
1431_at 2.735044747
1438_at 2.223399045
1487_at 10.11124976
1494_f_at 2.623144115
1552256_a_at 11.71768176
1552257_a_at 9.321973001
1552258_at 2.334780486
1552261_at 2.699661638
1552263_at 8.258715653
1552264_a_at 9.110751659
1552266_at 2.837292328

Total number of rows: 54675

Table truncated, full table size 1036 Kbytes.




Supplementary file Size Download File type/resource
GSM224701.CEL.gz 5.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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