Ontology highlight
ABSTRACT:
PROVIDER: PRJNA692381 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Small RNA sequencing was performed in woodland strawberry fruits for study of chromatin structure.
2024-09-25 | GSE208609 | GEO
Project description:Plethodontid salamanders are the largest family of salamanders and are classic models for studying the effect of rapidly evolving courtship pheromones on mating behavior and reproductive success. Despite interests in plethodontid reproduction, very little is known about the molecular composition of salamander gametes, as the extraordinary sizes of their genomes have impaired the development of various omic-scale resources. To identify what proteins may be expressed in salamander sperm, we performed DIA-MS on sperm samples from two plethodontid species, Plethodon shermani and Desmognathus ocoee. As the first detailed study of salamander sperm, this study partially fills in a critical taxonomic gap in the study of fertilization proteins in vertebrates.
2022-04-18 | PXD030143 | Pride
Project description:Global amphibian declines and extinction events are currently occurring at an unprecedented rate. While various factors are influencing these declines, one factor that is readily identifiable is disease. Specifically, the fungal pathogen Batrachochytrium dendrobatidis is thought to play a major role in amphibian declines in tropical and neotropical regions of the globe. While the effects of this chytrid fungus have been shown to be devastating, certain individuals and relict populations have shown resistance. This resistance has been attributed in part to the cutaneous microbiome. Many identified bacterial species that make up the microbiome have shown anti-B. dendrobatidis activity in vitro. One bacteria that is commonly associated as being a member of the amphibian microbiome across amphibian species and shows such anti-B. dendrobatidis activity is Serratia marcescens. Here, we look at transcriptomic shifts in gene expression of S. marcescens (high homology to strain WW4) in response to both live and heat-killed B. dendrobatidis.
2016-07-11 | GSE84057 | GEO
Project description:Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 hours post amputation. Many of the upregulated genes are predicted to function in wound healing and developmental processes, while many of the downregulated genes are typically expressed in muscle. The conserved transcriptional changes identified in this study provide a high-confidence dataset for identifying factors that simultaneous orchestrate wound healing and regeneration processes in response to injury, and more generally for identifying genes that are essential for salamander limb regeneration.
2018-07-10 | GSE116777 | GEO
Project description:Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 hours post amputation. Many of the upregulated genes are predicted to function in wound healing and developmental processes, while many of the downregulated genes are typically expressed in muscle. The conserved transcriptional changes identified in this study provide a high-confidence dataset for identifying factors that simultaneous orchestrate wound healing and regeneration processes in response to injury, and more generally for identifying genes that are essential for salamander limb regeneration.
2018-07-04 | GSE116615 | GEO
Project description:The order Caudata of amphibians has been important in the study of tissue regeneration. The most complete genetic available data from salamanders are from Ambystoma mexicanum (Ambystomidae) and Notophthalmus viridescens (Salamandridae). Transcriptome data obtained with Next-generation sequencing technology has become a useful tool to discover new candidate genes in non-model organisms without a genome of reference. This study highlights the need of performing RNA-sequencing in other salamander species to compare and identify important clusters of genes that could be modulating important biological process in amphibians. Here we describe a de novo reference transcriptome and its annotation of a non-model terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). For this purpose, we utilized genome protein databases from vertebrates, nucleotide sequences obtained for salamander species, and a de novo reference transcriptomes of Bolitoglossa ramosi to conduct a homology analysis. While the majority of the transcripts recovered homologs with Bolitoglossa ramosi, only a minority of the data (22%; n= 94,739) recovered homologs with other vertebrates. We also compared the transcriptome profile of skin tissue between these Bolitoglossa species. We found a group of antimicrobial peptides, such as cathelicidins, which have been not previously described in salamanders and could be important modulators of different biological process. All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015.
2019-12-07 | GSE107213 | GEO
Project description:Histone modifications mediate between genes and environment in plant growth and developmental events. To characterize the histone modification signatures in strawberry, we performed ChIP-seq experiments for seven histone marks in the immature and mature fruits, and leaves of the woodland strawberry F. vesca ('Ruegen'). The seven histone marks include H3K9/K14ac, H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3 and H3K9me2. In addition, to reveal the effect of the histone deacetylase FvHDA6, H3K9/K14a was profiled in FvHDA6-OE fruits.
2024-09-25 | GSE208638 | GEO
Project description:Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-seq to generate transcript sequence data and identify 602 genes that are differentially expressed during limb regeneration. This list was further processed to identify a core set of genes that exhibit conserved expression changes between B. ramosi and the Mexican axolotl (Ambystoma mexicanum), and presumably their common ancestor approximately 180 million years ago. Our study highlights the importance of developing comparative gene expression data for studies of limb regeneration among salamanders. All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015.
2018-09-26 | GSE105232 | GEO