Similar Datasets
Project description:To elucidate the complex physiological process of testis development and spermatogenesis in Sika deer, this study evaluated the changes of miRNA profiles in the four developmental stages of testis the juvenile (1-year-old), adolescence (3-year-old), adult (5-year-old) and aged (10-year-old) stages. The results showed that total total of 198 mature and 66 novel miRNAs were obtained. 88 (43 up and 45 down), 102 (44 up and 58 down), 54 (18 up and 36 down) DE miRNAs were identified in 3-vs.1-, 5-vs.3- and 10-vs.5-year-old testes, respectively. By integrating miRNA expression profiles, we predicted 69883 miRNA-mRNA interaction sites. The target genes were enriched by GO and KEGG pathways to obtain DE miRNA (miR-145, miR-140, miR-7, miR-26a, etc.), which play an important role in testis development and spermatogenesis. The data show that DE miRNAs could regulate testis developmental and spermatogenesis through signaling pathways, including MAPK signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, Hippo signaling pathway, etc. It provides a useful resource for future studies on the role of miRNA regulation in testis development and spermatogenesis.
2021-11-10 | GSE188369 | GEO
Project description:To elucidate the complex physiological process of testis development and spermatogenesis in Sika deer, this study evaluated the changes of mRNA profiles in the four developmental stages of testis the juvenile (1-year-old), adolescence (3-year-old), adult (5-year-old) and aged (10-year-old) stages. The results showed that total total of 23558 differentially expressed (DE) unigenes were obtained. 14918 (8413 up and 6505 down), 4988 (2453 up and 2535 down), 5681 (2929 up and 2752 down) DE unigenes were identified in 3-vs.1-, 5-vs.3- and 10-vs.5-year-old testes, respectively. By integrating mRNA expression profiles, we predicted 10790 mRNA-mRNA interaction sites. The target genes were enriched by GO and KEGG pathways to obtain DE mRNA (ALKBH5, Piwil, HIF1A, BRDT, etc.), which play an important role in testis development and spermatogenesis. The data show that DE mRNAs could regulate testis developmental and spermatogenesis through signaling pathways, including MAPK signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, Hippo signaling pathway, etc. It provides a useful resource for future studies on the role of genes regulation in testis development and spermatogenesis.
2021-11-10 | GSE188368 | GEO
Project description:Comparison of transcriptomes reveals differential regulation at four different ages in Sika Deer testes
| PRJNA778637 | ENA
Project description:Comparison of miRNA transcriptomes reveals differential regulation at four different ages in Sika Deer testes
| PRJNA778639 | ENA
Project description:Comparison of mRNA transcriptomes reveals differential regulation at four different ages in Sika Deer testes
| PRJNA778640 | ENA
Project description:To elucidate the complex physiological process of the growth, development and immunity response of Sika Deer, this study evaluated the changes of miRNA profiles in the four developmental stages (juvenile, adolescence, adult and aged) of ten tissue (adrenal, antler, brain, heart, kidney, lung, liver, skeletal muscle, spleen and testes). The results showed that a total of 306 known miRNAs and 143 novel miRNAs were obtained. Many miRNAs displayed organ-specificity and age-specificity. The largest number of miRNAs were enriched in the brain, some of which were shared only between the brain and adrenal. These miRNAs were involved in maintaining specific functions within the brain and adrenal. Additionally, the adolescence-adult transition of Sika Deer was a crucial stage in its life cycle. In conclusion, our study provided abundant data support for the current research Sika Deer. It also contributes to understand the role of miRNAs play in regulating the growth, development and immunity response of Sika Deer.
2022-09-06 | GSE212478 | GEO
Project description:Antler is a special bone tissue that has the ability to regenerate completely periodically. It is the fastest growing bone in the animal kingdom. Antler provides a valuable research model for bone growth and mineralization. Antler grows longitudinally by endochondral ossification with their growth center located in its tip. Many scholars have carried out detailed studies on morphology and gene expression of antler tip. However, few scholars have analyzed the protein expression patterns of antler tip at different development stages. This study used label-free proteomics approach to analyze the protein expression dynamics of the antler tip in six developmental periods (15, 25, 45, 65, 100 and 130 days after the previous antler cast) and costal cartilage. In result, 2052 proteins were confidently quantified, including 1937 antler proteins and 1044 costal cartilage proteins. Moreover, 913 antler core proteins and 132 antler-special proteins were obtained. Besides, the stages special proteins and differentially expressed proteins (DEPs) in different development stages were analyzed. A total of 875 DEPs were determined by one-way AVOVA. It is found that the growth period (15, 25, 45 and 65 days) showed more up-regulated protein including several chondrogenesis-associated proteins (collagen types II, collagen types XI, HAPLN1, PAPSS1 and PAPSS2). In ossification stages, the up-regulated proteins related with lysosome (CTSD, CTSB, MMP9, CAII) indicated that the antler has higher bone remodeling activity. Given the up-regulated expression of immune-related molecules (S100A7, CATHL7, LTF, AZU1, ELANE and MPO), we speculate that the local immune system may contribute to the ossification of antler tip. In conclusion, proteomics technology was used to deeply analyze the protein expression patterns of antler at different development stages. This provides a strong support for the research on the molecular regulation mechanism of rapid growth and ossification of velvet antler.
| S-EPMC8131589 | biostudies-literature
Project description:Increased ungulate browsing alters the composition of plant communities and modifies forest ecosystems worldwide. Ungulates alter their diet following changes in availability of plant species; however, we know little about how browse selection and plant community composition change with different stages of deer establishment. Here, we provide insight into this area of study by combining multiple approaches: comparison of the understory plant community, analysis of records of browsing damage, and DNA barcoding of sika deer feces at 22 sites in forests in northern Japan varying in when deer were first established. The coverage of vegetation and number of plant species were only lower at sites where deer were present for more than 20 years, while the difference in plant coverage among deer establishment years varied among plant species. Deer diet differed across establishment years, but was more affected by the site, thereby indicating that food selection by deer could change over several years after deer establishment. Plant life form and plant architecture explained the difference in plant coverage across establishment years, but large variability was observed in deer diet within the two categories. Integrating these results, we categorized 98 plant taxa into six groups that differed in vulnerability to deer browsing (degree of damage and coverage). The different responses to browsing among plant species inferred from this study could be a first step in predicting the short- and long-term responses of forest plant communities to deer browsing.
| S-EPMC8451445 | biostudies-literature
Project description:To determine whether Ehrlichia chaffeensis exists in Japan, we used PCR to examine blood from sika deer in Nara, Japan. Of 117 deer, 36 (31%) were infected with E. chaffeensis. The E. chaffeensis 16S rRNA base and GroEL amino acid sequences from Japan were most closely related to those of E. chaffeensis Arkansas.
| S-EPMC3044512 | biostudies-literature
Project description:BackgroundWith the unprecedented rapid growth rate (up to 2.75 cm/day), velvet antler is an invaluable model for the identification of potent growth factors and signaling networks for extremely fast growing tissues, mainly cartilage. Antler growth center (AGC) locates in its tip and consists of five tissue layers: reserve mesenchyme (RM), precartilage (PC), transition zone (TZ), cartilage (CA) and mineralized cartilage (MC). The aim of this study was to investigate the transcription dynamics in the AGC using RNA-seq technology.ResultsFive tissue layers in the AGC were collected from three 3-year-old male sika deer using our previously reported sampling method (morphologically distinguishable). After sequencing (15 samples; triplicates/tissue layer), we assembled a reference transcriptome de novo and used RNA-seq to measure gene expression profiles across these five layers. Nine differentially expressed genes (DEGs) were selected from our data and subsequently verified using qRT-PCR. The results showed a high consistency with the RNA-seq results (R2 = 0.80). Nine modules were constructed based on co-expression network analysis, and these modules contained 370 hub genes. These genes were found to be mainly involved in mesenchymal progenitor cell proliferation, chondrogenesis, osteogenesis and angiogenesis. Combination of our own results with the previously published reports, we found that Wnt signaling likely plays a key role not only in stimulating the antler stem cells or their immediate progeny, but also in promoting chondrogenesis and osteogenesis during antler development.ConclusionWe have successfully assembled a reference transcriptome, generated gene expression profiling across the five tissue layers in the AGC, and identified nine co-expressed modules that contain 370 hub genes and genes predorminantly expressed in and highly relevant to each tissue layer. We believe our findings have laid the foundation for the identification of novel genes for rapid proliferation and chondrogenic differentiation of antler cells.
| S-EPMC6402185 | biostudies-literature