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ABSTRACT:
PROVIDER: PRJNA1091038 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goal of this study is to compare (RNA-seq) transcriptomes of in vitro cultured human bone marrow-derived mesenchymal stem cells (hMSCs) and fallow deer antler-derived skeletal progenitors (FD RM Cells) under multiple conditions to identify candidate proliferation and mineralization genes responsible for fast antler regeneration Methods: hMSCs and FD RM Cells were cultured in vitro under 1) serum-free (0% serum) or serum (10% serum) conditions for 2.5 days or 2) Control (0 ng/mL BMP-2 and 0 nM dexamethasone) and osteogenic (100 ng/mL BMP-2 and 100 nM dexamethasone) media for 24 days. mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads were analyzed at the transcript isoform level STARS followed by Cufflinks. Validation for genes of interest was performed using immunofluorescence staining. Results: Comparison of human and fallow deer skeletal progenitor datasets yielded proliferation and mineralization gene candidates Conclusions: Our study represents the first detailed analysis of human and fallow deer transcriptomes of skeletal progenitor cells under proliferation and mineralization conditions, with biologic replicates, generated by RNA-seq technology. Our in vitro comparative approach circumvent some of the logistical and technical challenges in identifying candidate proliferation and mineralization genes responsible for rapid deer antler regeneration. We conclude that in vitro comparison of RNA-seq based transcriptomes identified candidate proliferaiton and mineralization genes to advance bone biology and holds promise to rapidly regenerate large bone volumes for regenerative medicine. The comparative approach utilized here can be adapted for almost any tissue to study a specific phenomenon of interest.
2018-11-16 | GSE89796 | GEO
Project description:A Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 1 MTD project_description Many diseases have been associated with gut microbiome abnormalities. The root cause of such diseases is not only due to bacterial dysbiosis, but also to change in bacterial functions, which are best studied by proteomic approaches. Although bacterial proteomics is well established, metaproteomics is hindered by challenges associated with the sample physical structure, contaminating proteins, the simultaneous analysis of hundreds of species and the subsequent data analysis. Here, we present a systematic assessment of sample preparation and data analysis methodologies applied to LC-MS/MS metaproteomics experiment. We could show that low speed centrifugation (LSC) has a significant impact on both peptide identifications and reproducibility. LSC led to increase in peptide and proteins identifications compare to no LSC. Notably, the dominant bacterial phyla, i.e. Firmicutes and Bacteroidetes, showed divergent representation between LSC and no-LSC. In terms of data processing, protein sequence databases derived from mouse faeces metagenome provided at least four times more MS/MS identification compared to databases of concatenated single organisms. We also demonstrated that two-steps database search strategy comes at the expense of a dramatic rise in number of false positives compared to single-step strategy. Overall, we found a positive correlation between matching metaproteome and metagenome abundance, which could be linked to core microbial functions, such as glycolysis-gluconeogenesis, citrate cycle and carbon metabolism. We observed significant overlap and correlation at the phylum, class, order and family taxonomic levels between taxonomy-derived from metagenome and metaproteome. Notably, nearly all functional categories (e.g., membrane transport, translation, transcription) were differentially abundant in the metaproteome (activity) compared to what would be expected from the metagenome (potential). In conclusion, these results highlight the need to perform metaproteomics when studying complex microbiome samples.
2022-02-16 | PXD021932 | Pride
Project description:Studies of the miRNA expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the differential expression of miRNAs from skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer. A total of 171 known miRNAs and 60 novel miRNAs were identified based on four small RNA libraries. 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 4 miRNAs were differentially expressed between adult and adolescence sika deer, and 1 miRNAs were differentially expressed between aged and adult sika deer. GO and KEGG analyses showed that miRNA were mainly related to energy and substance metabolism, processes that are closely associate with growth, development and aging of skeletal muscle. We also constructed mRNA-mRNA and miRNA-mRNA interaction networks related to growth, development and aging of skeletal muscle. The results showed that miR-133a, miR-133c, miR-192, miR-151-3p etc. may play important roles in muscle growth and development, and miR-17-5p, miR-378b, miR-199a-5p, miR-7 etc. may have key roles in muscle aging. In this study, we determined the dynamic miRNA in muscle tissue for the first time in sika deer. The age-dependent miRNAs identified will offer insights into the molecular mechanism underlying muscle development, growth and maintenance and also provide valuable information for sika deer genetic breeding.
2020-01-11 | GSE142978 | GEO