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Sample GSM224699 Query DataSets for GSM224699
Status Public on Feb 05, 2016
Title Caco-2 S1400-1
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 11.49896384
1053_at 8.79269272
117_at 2.457338964
121_at 6.261695636
1255_g_at 2.203820372
1294_at 2.000823489
1316_at 2.89296136
1320_at 6.806474694
1405_i_at 3.413495707
1431_at 2.688442358
1438_at 2.181760221
1487_at 10.298715
1494_f_at 2.547553842
1552256_a_at 12.32492268
1552257_a_at 9.992407376
1552258_at 2.269971086
1552261_at 2.651483955
1552263_at 7.680065332
1552264_a_at 9.740033738
1552266_at 2.714325844

Total number of rows: 54675

Table truncated, full table size 1035 Kbytes.




Supplementary file Size Download File type/resource
GSM224699.CEL.gz 5.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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