Similar Datasets
Project description:Objective: The purpose of this study is to describe colonic cells differential transcriptomes and cellular pathways directly modulated by exposure to prebiotics. Prebiotic oligosaccharides are widely used as animal and human in-feed additives for their beneficial effects on the probiotic gut microbiota. A number of studies have revealed a protective effect of several oligosaccharides on dysfunctional or challenged intestinal cells models through microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods. However, thus far there was limited data assessing the direct effect of such functional foods on on whole-transcriptome of unchallenged intestinal epithelial cells. Methods: Colonic mRNA profiles of confluent Caco-2 cells exposed for 24h to GOS or FOS and their respective mono- and di-saccharides mock treatments were generated for 3 biological replicates. Library pool was sequenced on the Illlumina NextSeq500 over two NextSeq500 High Output 150 cycle kits (Illumina; FC-404-2002). Sequence reads were quality checked with FastQC (version 0.11.3). Using CLC Genomics Workbench 12.03, sequences were trimmed from adaptor, paired and good quality sequence read pairs were mapped to the Homo sapiens GRCh38 reference genome (Hg38). Transcripts counts were normalised and differential gene expression analysed using the RNAseq Analysis Module of CLC Genomics Workbench 12.03. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis were developed to investigate the statistically significant gene sets (|FC value ≥ 1.5, FDR p-adj. < 0.05) by implementing the NIPA Enrichment R script (v0.6.7.R, https://github.com/ADAC-UoN/NIPA). RNAseq results were validated by qRT–PCR assays. Results: Sequencing generated between 45 to 134 million of 75-bp paired-end sequence reads per sample. An average of 58 million sequence reads per sample were paired and mapped to human genes (genome Homo sapiens GRCh38). For GOS exposure, 89 genes were differentially expressed (fold-change ≥ 1.5 and q-value < 0.05) between GOS and mock-treated groups. Gene ontology functional analysis revealed that genes up-regulated in the presence of GOS were involved in digestion, absorption, transmembrane transport whereas genes involved in drug and xenobiotic metabolic processes were reduced. With FOS treatment, 12 genes were differentially expressed (fold-change ≥ 1.5 and q-value < 0.05) relative to the control group and functional analysis of enriched GO terms revealed up-regulated DEGs were associated with steroid metabolic process. Conclusions: Our study details the first whole-transcriptome analysis of colonic epithelial cells exposed to the direct effect of prebiotics GOS and FOS. Our RNA-seq based characterization of distinctive or shared differentially expressed genes and enriched pathways generated for GOS and FOS would support further network analyses and enable the examination of intricate biological functions within more complex environments.
2020-02-15 | GSE145303 | GEO
Project description:Daphnia pulex strain:GOS-1 Genome sequencing
| PRJNA212131 | ENA
Project description:Our study in mice investigated the potential effects of the prebiotics GOS and inulin administrated during gestation on the development of DSS-induced chronic colitis in the offspring. Mothers were given or not during gestation a diet enriched in the prebiotics GOS and inulin. Eight to ten weeks old male offspring were treated or not with 3 cycles of DSS in drinking water, one cycle consisting of 2 days with DSS and 5 days without DSS.
2022-12-15 | E-MTAB-12176 | biostudies-arrayexpress
Project description:Transcriptome analysis of Bifidobacterium pseudocatenulatum CECT 7765 growing with Galacto-oligosaccharides (GOS) as carbon source.
| PRJEB6928 | ENA
Project description:Lactulose-derived oligosaccharides (OsLu) are prebiotic galactooligosaccharides (GOS) known to be beneficial for human health. Many of these carbohydrates are reported to have immunomodulatory properties; however the molecular mechanism is unclear. OsLu produced by enzymatic synthesis can be purified with Saccharomyces cerevisiae (OsLu-Sc). We show that this purification method introduces yeast-derived proteins reactive to Dectin-2, an innate immune receptor for fungal polysaccharides. Using a cell-based bioassay, we tested the binding of OsLu and GOS samples to Dectin-2. While OsLu purified with active charcoal and commercial GOS failed to bind to Dectin-2, we found OsLu-Sc bound to this receptor. The carbohydrate-binding incompetent mutant of Dectin-2 failed to bind to OsLu-Sc. These data suggest that OsLu-Sc introduced carbohydrate ligands for Dectin-2. In accordance with this, proteomic analysis revealed OsLu-Sc contained S. cerevisiae-derived mannoproteins. Therefore, our data highlights the importance of the purification method for OsLu, which may positively affect the bioactivity of OsLu.
2018-12-11 | PXD010495 | Pride
Project description:Glioblastoma is one of the deadliest malignancies worldwide and is virtually incurable due to its highly infiltrative growth and limited sensitivity to conventional treatment by radiochemotherapy. It is hypothesized that a small population of cells with a stem-like phenotype is the major culprit of tumor recurrence. These cells are characterized by an enhanced DNA repair capacity and expression of stemness marker genes, and elimination of this population might delay or even stop tumor recurrence following radiochemotherapy. The aim of this study was to analyze whether interference with the Hedgehog signaling (Hh) pathway or combined Hh/Notch blockade can efficiently target these cancer stem cells and sensitize them to chemotherapeutic drugs. Using tumor sphere lines and primary glioma cells we demonstrate that the Hh pathway inhibitor GANT61 (GANT) and the Hh/Notch inhibitor arsenic trioxide (ATO) are capable to synergistically decrease proliferation and induce cell death in combination with the natural cotton derived anticancer agent (-)-Gossypol (Gos). In contrast to GANT in combination with Gos, the ATO/Gos combination also strongly prevented sphere formation and recovery. These synergistic effects were associated with major proteomic changes indicating decreased cell movement, distortion of cell cycle and DNA repair, as well as markedly reduced stemness. Collectively, our data show that ATO and Gos, two drugs that are safe for use in humans, represent a promising targeted therapy approach for the synergistic and specific elimination of glioma stem-like cells.
2019-03-13 | PXD009249 | Pride
Project description:Relative mRNA levels of 27 genes were evaluated with the SYBR Green qPCR assays after gossypol (Gos) treatment for 2-24 h.
2022-05-15 | GSE203027 | GEO
Project description:To identify the differentially expressed genes in normal gastric mucosa and gastric cancer tissues, we employed the microarray profiling analysis. Genes with greater than 2-fold change and P-value ＜0.05 were identified as differentially expressed genes. From this dataset, we obtained differentially expressed genes by cluster analysis and enriched GOs was identified by Gene set enrichment analysis (GSEA) analysis, microtubule GO was one of the most enriched GOs, and the gene KIF14 was selected to go on to the next step in the study.
2018-08-23 | GSE118897 | GEO
Project description:Next generation sequencing transcriptome analysis of polarized colonic Caco-2 cells exposed to prebiotics GOS and FOS
| PRJNA606703 | ENA