|
| Status |
Public on Mar 11, 2013 |
| Title |
T84_butyrate8mM |
| Sample type |
RNA |
| |
|
| Source name |
T84 human colonic carcinoma epithelial cells, treated with 8mM butyrate for 24 hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T84
cell type: colonic carcinoma epithelial cells
treatment: 8mM butyrate
treatment duration: 24 hrs
|
| Treatment protocol |
T84 cells were treated with rosiglitazone (0.1 μM) or butyrate (1 mM or 8 mM) for 24 hrs. Non-treated cells served as the control.
|
| Growth protocol |
T84 human colonic carcinoma epithelial cells were cultured in DMEM F-12 medium (Lonza, the Netherlands) containing 5% fetal calf serum (FCS) and 1% penicillin/streptomycin at 37°C in a humidified incubator of 95% air/5% CO2. Cells were grown till 80-90% confluence before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using TRIzol reagent (Invitrogen), whereafter purified total RNA was isolated using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For microarray analysis, RNA samples from 3 wells per treatment were pooled.
|
| Label |
biotin
|
| Label protocol |
One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT Expression Kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
|
| |
|
| Hybridization protocol |
Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument according to the manufacturer's recommendations.
|
| Description |
G052_H07_T5_8B.CEL
Pool of 3 cell culture wells.
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).
|
| |
|
| Submission date |
Sep 07, 2012 |
| Last update date |
Mar 11, 2013 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
guido.hooiveld@wur.nl
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11532 |
| Series (1) |
| GSE40706 |
Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colonocytes by selective PPARγ modulation |
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