Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression data from HT-29, a human colonic epithelial cell line

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Protim Sarker

PROVIDER: E-GEOD-45220 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Diabetic nephropathy (DN) as a common complication of diabetes is the primary cause of end-stage renal disease. Sodium butyrate (NaB) is a short chain fatty acid in the metabolic products of intestinal bacterium, and its kidney protective effect has been reported in DN. However, its underlying mechanism remains unclear. The aim of the present study was to investigate the effect of NaB on globe transcriptome changes in DN. In our study, eight-week-male db/db mice which were established DN mice were randomly divided into two groups: the DN+NaB group (DN mice treated with NaB, 5g/kg/day) and the DN group (DN mice treated with saline). Also, the normal db/m mice were used as NC group. Further, blood glucose, body weight, urinary microalbumin and urinary creatinine of mice were measured in three groups. Whole-transcriptome analysis was performed by RNA sequencing (RNA-Seq) to evaluate profiling of lncRNAs and messenger RNAs (mRNAs). Bioinformatic analysis was performed to predict the potential NaB-related lncRNAs and genes in DN. The expressions of lncRNAs and mRNAs were tested by quantitative real-time polymerase chain reaction (qRT-PCR) in renal tissues and mesangial cells treated with NaB. The results of the present study demonstrated that NaB ameliorated renal dysfunction in DN mice. Moreover, RNA-Seq results identified that 17 lncRNAs and 180 mRNAs reversely changed in DN+NaB group when compared with those in DN group. Additionally, the integrated co-expression networks of NaB-related lncRNAs revealed these lncRNAs interacted with 155 key mRNAs. The co-expression networks of mRNAs associated to immune response, antigen processing and presentation and acute inflammatory response to antigenic stimulus. The qRT-PCR data showed that eight mRNAs and seven lncRNAs were dysexpressed by NaB in DN mice and mesangial cell under high glucose condition. Furthermore, the co-expression network of inflammation related lncRNAs and mRNAs demonstrated that those 17 reversed lncRNAs and 37 mRNAs also play essential roles in inflammatory response. In summary, the present study suggests that NaB ameliorates diabetes induced renal dysfunction and regulates transcriptome changes in DN. NaB related lncRNA-mRNA may play roles in the protective effect of NaB in DN.

Dataset Information

Expression data from HT-29, a human colonic epithelial cell line

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure