RNA-Seq of sika deer antler-tip during the ossification stage
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ABSTRACT: To obtain an overview of the antler tip gene expression profile during rapid growth period, a cDNA sample was prepared from antler tip and sequenced using the Illumina sequencing platform.
Project description:To obtain an overview of the antler tip gene expression profile during the ossification stage, a cDNA sample was prepared from antler tip and sequenced using the Illumina sequencing platform.
Project description:Deer antlers are amazing natural appendages that grow faster than any other known mammalian bone. Antler growth occurs at the tip and is initially cartilage, which is later replaced by bone tissue. However, little is known regarding the precise role of cooperation between cell lineages and functional genes in regulating antler growth, and molecular mechanisms responsible for rapid growth remain elusive. In this study, we use an RNA-Seq approach to identify miRNA expression patterns during antler growth.
Project description:We used label-free proteomics approach to analyze the protein expression dynamics of the antler tip in 6 developmental periods (15, 25, 45, 65, 100 and 130 days after the previous antler cast) and costal cartilage. the stages special proteins and differentially expressed proteins (DEPs) in different development stages were analyzed.
Project description:The velvet antler is a unique model for cancer and regeneration research due to its periodic re-generation and rapid growth. Antler growth is mainly triggered by the growth center located in its tip, which consists of velvet skin, mesenchyme and cartilage. Among them, cartilage accounts for most of the growth center. We performed an integrative analysis of the antler cartilage tran-scriptome and proteome at different antler growth stages. RNA-seq results revealed 24,778 uni-genes, 19,243 known protein-coding genes, and 5,535 new predicted genes. Of these, 2,722 were detected with differential expression patterns among 30 d, 60 d, and 90 d libraries, and 488 dif-ferentially expressed genes (DEGs) were screened at 30 d vs. 60 d and 60 d vs. 90 d but not at 30 d vs. 90 d. Proteomic data identified 1,361 known proteins and 179 predicted novel proteins. Compar-ative analyses showed 382 differentially expressed proteins (DEPs), of which 16 had differential expression levels at 30 d vs. 60 d and 60 d vs. 90 d but not at 30 d vs. 90 d. An integrated analysis conducted for DEGs and DEPs showed that gene13546 and its coding protein protein13546 anno-tated in the Wnt signaling pathway may possess important bio-logical functions in rapid antler growth. This study provides in-depth characterization of candidate genes and proteins, providing further insights into the molecular mechanisms controlling antler development.
Project description:Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq Technology
Project description:The aim of the study is to characterize the gene expression of the growing antlers during their process of regeneration and fast growth Experiment Overall Design: Gene profiles of RNA samples from antler tip, base (pedicle) and frontal bone. Samples were harvested during spring, at the period of maximum antler growth (60 days after casting the previous antlers). And additional sample (DEER4) was harvested at the end of the growing season (90 days after the casting).
Project description:To study genes specially expressed in root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) of Ceratopteris richardii, we carried out an RNA-seq to analyze gene expression levels from these five tissues.
Project description:we used proteomic technology to disclose the difference of antler regeneration between red deer and sika deer. Through functional analysis, we obtained differentially expressed proteins and the pathway involved in antler regeneration between two groups
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.
Project description:Identification of the changes in gene expression between the antler velvet and mesenchyme, pedicle skin and frontal skin tissues from adult male deers (Cervus elaphus). Hybridization data were analysed using MAS5, RMA, GCRMA and Dchip algorithms to maximize the chances of identifying gene expression changes.