Dataset Information

Evaluation of the potential of 4 micro algae extracts to modulate the immune response and metabolic state in intestinal epithelium cells

ABSTRACT: Micro algae's are used as alternative protein source in human and animal diets. Besides micro algae contain substantial amounts of proteins they also contain a high concentration of, often unique, biological and chemical substances with potential to induce beneficial and health promoting effects in humans and animals. This study was set up to evaluate the potential of these substances to improve (intestinal) health. The effect of extracts prepared from 3 monocultures of micro algae's (Chlorella vulgaris [C], Haematococcus pluvialis [H], and Spirulina platensis [S]) and a mixed culture of micro algae's (AM; a mixture of Scenedesmus sp. and Chlorella sp. ) was studied in the presence and absence of the enterotoxigenic bacterium Escherichia coli k99 strain (ETEC, [E]) as an in vitro challenge. The E.coli-k99 strain with adhesion factor F41 (41/32) was isolated from a mastitis-infected udder. Gene expression was measured in cultured intestinal porcine epithelium cells (IPECJ2 cell line) after 2 and 6 hours incubation with C, H, and S extracts, and after 6 hours with the AM extract, using “whole genome” porcine microarrays. Gene expression profiles were analysed using functional bioinformatics programs to provide insight in the biological processes induced by micro algae extracts.

ORGANISM(S): Sus scrofa

PROVIDER: GSE113365 | GEO | 2019/03/14

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:By applying Illumina Novaseq 6000, Chlorella sp. TLD6B cells of the control group on day zero and 18, as well as under low salt stress (NaCl1) and under high salt stress (NaCl2) on day 18 were selected for transcriptome sequencing analysis. Meanwhile, 0.05 g/mL ( PEG1) and 0.1 g/mL PEG-6000 (medium for drought stress, PEG2 ) were used to prepare the drought-stressed Chlorella sp. TLD6B cells. Each treatment had two replicates. Clean data were filtered after the removal of adapters, poly-N strands, and low-quality reads. There were no reference genomes for Chlorella sp. TLD6B, and de novo assembly for clean reads was performed by using Trinity. The sequences were compared with databases such as NR, NT, Swiss-Pro, GO, KEGG, PFAM, and KOG using Blast X (e-value ≤ 10-5). The GO annotation of unigenes was obtained using BLAST2GO. FPKM method was used for the analysis of gene expression levels (Trapnell et al., 2010). Out of six samples, a total of 963,078,184 raw reads were generated. A total of 947,225,244 clean reads were obtained based on the base quality score and read length. Meanwhile, the GC percentage in clean reads reached nearly 66.0%, with Q20 being above 96%. A total of 219,577 transcripts with an average length of 1,394 bp were obtained. In total, 155,503 non-redundant unigenes were assembled for the following analyses. The length of the unigenes ranged from 200 bp to 23,825 bp, with an average length of 1,842 bp. Under different salt stress, verification had been conducted with qRT-PCR on nine unigenes of different pathways, which were related to lipid metabolism. The detection results by qRT-PCR were highly correlated with RNA-Seq results (r = 0.890, r2 = 0.791), which indicated that the RNA-Seq data of Chlorella sp. TLD6B under salt stress were accurate and reliable. Our study represents the first detailed analysis of Chlorella sp. TLD6B under salt stress transcriptomes. Hierarchical clustering of differentially expressed genes uncovered several currently uncharacterized genes that may contribute to the function about lipid accumulation of Chlorella sp. TLD6B under salt stress.

Project description:Intestinal lymphocytes are crucial members of the mucosal immune system with impact over outcomes of intestinal health versus dysbiosis. Resolving intestinal lymphocyte complexity and function is a challenge, as the intestine provides cellular snapshots of a diverse spectrum of immune states. In pigs, intestinal lymphocytes are poorly described relative to humans or traditional model species. Enhanced understanding of porcine intestinal lymphocytes will promote food security and improve utility of pigs as a biomedical model for intestinal research. Single-cell RNA sequencing (scRNA-seq) was performed to provide transcriptomic profiles of lymphocytes in porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation revealed previously undescribed cells in porcine intestine, including SELLhi gd T cells, group 1 and group 3 innate lymphoid cells (ILCs), and four subsets of B cells. Single-cell transcriptomes in ileum were compared to those in porcine blood, and subsets of activated lymphocytes were detected in ileum but not periphery. Comparison to scRNA-seq human and murine ileum data revealed a general consensus of ileal lymphocytes across species. Lymphocyte spatial context in porcine ileum was conferred through differential tissue dissection prior to scRNA-seq. Antibody-secreting cells, B cells, follicular CD4 ab T cells, and cycling T/ILCs were enriched in ileum with Peyer’s patches, while non-cycling gd T, CD8 ab T, and group 1 ILCs were enriched in ileum without Peyer’s patches. scRNA-seq findings were leveraged to develop advanced toolsets for further identification of ILCs in porcine ileum via flow cytometry and in situ staining. Porcine ileal ILCs identified via scRNA-seq did not transcriptionally mirror peripheral porcine ILCs (corresponding to natural killer cells) but instead had gene signatures indicative of tissue- and activation-specific functions, indicating potentially similar roles to intestinal ILCs identified in humans. Overall, the data serve as a highly-resolved transcriptomic atlas of the porcine intestinal immune landscape and will be useful in further understanding intestinal immune cell function.

Dataset Information

Evaluation of the potential of 4 micro algae extracts to modulate the immune response and metabolic state in intestinal epithelium cells

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure