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Sample GSM224711 Query DataSets for GSM224711
Status Public on Feb 05, 2016
Title Caco-2 Flagellin-1
Sample type RNA
 
Source name 2 h with 100 ng recombinant flagellin
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 100 ng recombinant flagellin.
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 11.89880754
1053_at 8.79133014
117_at 2.41160556
121_at 6.251902977
1255_g_at 2.202641604
1294_at 2.01021947
1316_at 2.961848911
1320_at 7.364784306
1405_i_at 3.476141785
1431_at 2.622447267
1438_at 2.175652925
1487_at 10.45315121
1494_f_at 2.583309137
1552256_a_at 11.6664933
1552257_a_at 9.975872373
1552258_at 2.256363447
1552261_at 2.596857193
1552263_at 7.997465761
1552264_a_at 10.07510206
1552266_at 2.753777811

Total number of rows: 54675

Table truncated, full table size 1035 Kbytes.




Supplementary file Size Download File type/resource
GSM224711.CEL.gz 5.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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