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Sample GSM224708 Query DataSets for GSM224708
Status Public on Feb 05, 2016
Title Caco-2 EAV9-3
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 10.72673532
1053_at 8.830415938
117_at 2.488853811
121_at 6.376099917
1255_g_at 2.259531488
1294_at 2.044469751
1316_at 2.954207955
1320_at 6.167573349
1405_i_at 3.57670995
1431_at 2.726005544
1438_at 2.219048313
1487_at 10.43287755
1494_f_at 2.613027211
1552256_a_at 11.71388835
1552257_a_at 9.355054942
1552258_at 2.327348444
1552261_at 2.697775503
1552263_at 7.085320778
1552264_a_at 8.833992029
1552266_at 2.840265726

Total number of rows: 54675

Table truncated, full table size 1035 Kbytes.




Supplementary file Size Download File type/resource
GSM224708.CEL.gz 5.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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