Comment[ArrayExpressAccession]	E-GEOD-45220
MAGE-TAB Version	1.1							
Public Release Date	2013-03-16
Investigation Title	Expression data from HT-29, a human colonic epithelial cell line							
Comment[Submitted Name]	Expression data from HT-29, a human colonic epithelial cell line
Experiment Description	Gene(s) in epithelial cells can be upregulated or downregulated by different stimuli in a tissue-specific manner. We used genome-wide microarray analysis to profile the expression of genes in HT-29 cells that are upregulated after stimulation with sodium butyrate (NaB) and subsequently downregulated by the addition of ciprofloxacin antibiotic. The specific aim was to evaluate genes that are associated with mucosal immunity. HT-29 cells were stimulated with sodium butyrate (NaB) (n=3), NaB and ciprofloxacin (n=3) or culture media (unstimulated control, n=3) for 24 hours. RNA extracted from these cells were hybridized on Affymetrix microarrays.							
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl						
Person Last Name	Sarker							
Person First Name	Protim							
Person Email	protim@icddrb.org							
Person Affiliation	icddr,b							
Person Phone	+8801772683211							
Person Address	icddr,b, Mohakhali, Dhaka, Bangladesh							
Person Roles	submitter							
Protocol Name	P-GSE45220-1	P-GSE45220-6	P-GSE45220-3	P-GSE45220-8	P-GSE45220-7	P-GSE45220-2	P-GSE45220-4	P-GSE45220-5
Protocol Description	ID_REF =  VALUE = Quantitative signal	Hybridization to Human Gene 1.1 ST array plates was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.	HT-29 (ATCC, HTB-38) was grown up to 80-90% confluence in culture medium (RPMI-1640 supplemented with 10% fetal calf serum, 25 mM HEPES, 2 mM L-glutamine amd penicillin-streptomycin [Invitrogen]) in 6-well tissue culture plates (Corning) at 37C in 5% CO2.	Preprocessing in Affymetrix Expression Console (v 1.1) using the following methods. Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.	Array plates were scanned using a GeneTitan scanner.	Culture media was discarded, cells were rinsed with PBS and stimulated with 2 mM NaB (Sigma) alone or in combination with 125/150 ug/ml ciprofloxacin (Sigma) in culture medium in the absence of fetal calf serum and penicillin-streptomycin for 24 hours at 37C in 5% CO2. Cells incubated with only culture medium served as an unstimulated control.	Extraction of RNA from cells was performed utilizing the RNeasy RNA purification kit according to the manufacturer's instructions (Qiagen).	Total RNA was converted to sense strand cRNA using the Ambion WT expression kit. For fragmentation and labeling, the GeneChip WT Target Labeling kit was used.
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	TREATMENT							
Experimental Factor Type	treatment							
Comment[SecondaryAccession]	GSE45220							
Comment[GEOReleaseDate]	2013-03-16							
Comment[ArrayExpressSubmissionDate]	2013-03-15							
Comment[GEOLastUpdateDate]	2013-03-17							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-45220.sdrf.txt