RNA-seq analysis of vehicle and DOPPA-treated human cord blood CD34+ cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE131092 | GEO | 2021/09/30
REPOSITORIES: GEO
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2012-05-09 | E-GEOD-30503 | biostudies-arrayexpress
Project description:A common method used both in vitro and in vivo, to identify Tregs in CD4+ T cells is through the characterization of surface marker CD25. Although CD25 expression is well correlated with regulatory activity in vitro, CD4+CD25+ T cells are not the only regulatory CD4+ T cells in vivo. Studies suggest that in many situations, CD4+CD25– T cells are as effective as CD4+CD25+ T cells in controlling T cell mediated disease. Therefore, CD25 is not a uniquely specific cell surface marker for the identification of Tregs. CD49f is an α6-integrin subunit which dimerizes with either the β 1 or β 4 subunit to form receptors for various laminin isoforms. We found that CD4+ T cells from NOD mice express CD49f, and old non-diabetic NOD mice had an increase of CD4+CD49f+ T cells in the spleen and peripheral lymph node when compared to both young and diabetic mice. This study was conducted to further characterize CD4+CD49f+ Treg cell subpopulation in NOD mice. It was found that CD4+CD49f+T cells possess suppressive ability and only one third of CD4+CD49f+ T cells expressing CD25. Based on the expression of CD49f and CD25, CD4+ T cells was divided into four populations , CD25+CD49f+ ,CD25+CD49f- ,CD25-CD49f+ but CD25-CD49f- are of suppressive ability, and we further found that Foxp3 expression was highly correlated with the suppressive ability of these three Treg populations. In conclusion our data indicate that CD49f marks a CD4+ CD25+ Treg subset with more potent suppression activity and identifies a CD25-CD4+ T cell population with suppression function in a Foxp3+ expression dependent manner.
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2018-08-23 | GSE118897 | GEO
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2017-11-09 | GSE106664 | GEO
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.
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Project description:Purpose: miRNAs, a member of the small RNA, play critical roles in the mammalian spermatogenesis. Spermatogonia was the foundation of spermatogenesis and valuable for the study of spermatogenesis. However, it is still not clear that the expression profiling of the miRNAs in spermatogonia of dairy goat. Methods: The CD49f was one of the surface markers for spermatogonia enrichment by MACS. Therefore, we used CD49f microbeads antibody to purify CD49f-positive and negative cells of dairy goat testicular cells by MACS (Magnetic Activated Cell Sorting), and then in-depth analyzed the miRNA expression in these cells using Illumina sequencing technology. Results: The results of miRNAs expression profiling in purified CD49f-positive and negative testicular cells showed that 933 were miRNAs upregulated in CD49f-positive cells and 916 were miRNAs upregulated in CD49f-negative cells with a 2-fold increase, respectively; some spermatogonial stem cells(SSCs) specific miRNAs and marker genes in testis had a higher level expression in CD49f-positive testicular cells, such as miR-221, miR-23a, miR-29b, miR-24, miR-29a, miR-199b, miR-199a, miR-27a, miR-21. Conclusions: our comparative miRNAome data provided some useful miRNAs profiling data of dairy goat spermatogonia cells and suggested CD49f could be used to enrich dairy goat spermatogonia-like cells, including SSCs.
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Project description:Purpose: miRNAs, a member of the small RNA, play critical roles in the mammalian spermatogenesis. Spermatogonia was the foundation of spermatogenesis and valuable for the study of spermatogenesis. However, it is still not clear that the expression profiling of the miRNAs in spermatogonia of dairy goat. Methods: The CD49f was one of the surface markers for spermatogonia enrichment by MACS. Therefore, we used CD49f microbeads antibody to purify CD49f-positive and negative cells of dairy goat testicular cells by MACS (Magnetic Activated Cell Sorting), and then in-depth analyzed the miRNA expression in these cells using Illumina sequencing technology. Results: The results of miRNAs expression profiling in purified CD49f-positive and negative testicular cells showed that 933 were miRNAs upregulated in CD49f-positive cells and 916 were miRNAs upregulated in CD49f-negative cells with a 2-fold increase, respectively; some spermatogonial stem cells(SSCs) specific miRNAs and marker genes in testis had a higher level expression in CD49f-positive testicular cells, such as miR-221, miR-23a, miR-29b, miR-24, miR-29a, miR-199b, miR-199a, miR-27a, miR-21. Conclusions: our comparative miRNAome data provided some useful miRNAs profiling data of dairy goat spermatogonia cells and suggested CD49f could be used to enrich dairy goat spermatogonia-like cells, including SSCs. miRNA profiles of goat CD49f-positive and negative testicular cells were generated by deep sequencing, in triplicate, using Illumina GAIIx
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