Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome data of the interdigital webbing in Chinese Soft-shell Turtle (Pelodiscus sinensis)

ABSTRACT: Transcriptome data of the interdigital webbing in Chinese Soft-shell Turtle (Pelodiscus sinensis)

PROVIDER: PRJNA1211067 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32009620_1.fastq.gz	Fastqsanger.gz
	SRR32009620_2.fastq.gz	Fastqsanger.gz
	SRR32009621_1.fastq.gz	Fastqsanger.gz
	SRR32009621_2.fastq.gz	Fastqsanger.gz
	SRR32009622_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Transcriptome data of the interdigital webbing in Chinese Soft-shell Turtle (Pelodiscus sinensis)

Project description:interdigital cell death (ICD) is an essential role in amniotes to promote the regression of interdigital tissue for digits separation. Antagonizing this process can lead to the formation of webbed limbs. However, the mechanism of forming webbed limbs is not the same among independently evolved species, and the reason is still unclear. The Chinese softshell turtle (Pelotiscus sinensis) is a good research model, exhibiting a transitional feature from no webbed to fully webbed. In this study, we collected 8 samples of interdigital webbing from the forelimbs and hindlimbs of turtles at embryonic stage 19 (TK19) for RNA sequencing. We identified 608 potential regulatory genes through differential expression analysis. These findings not only provide new perspectives and data support for comparative studies of adaptive convergent evolution in aquatic animals, but also enhance our understanding of the mechanisms underlying quadrupedal limb morphology. In addition, these results provide potential molecular targets for studying the plasticity of programmed cell death or aging.

2025-05-08 | GSE287055 | GEO

Environmentally relevant concentrations of niclosamide disrupt antioxidant defense, histology, and the liver and intestine transcriptome of Chinese soft-shelled turtle

Project description:To investigate the cellular responses of the Chinese soft-shelled turtle after niclosamide exposure, a total of 45 healthy juvenile turtles randomly selected and divided into three groups containing one control group (without NIC exposure, CG) and two experimental groups (exposed to 10 and 50 μg/L of NIC, respectively).

2024-01-01 | GSE225631 | GEO

Wild type and probiotic feeding transcriptome of pelodiscus sinensis

Project description:In recent years, the scale culture of Chinese soft-shelled turtle has developed rapidly. However, diseases in aquaculture are the main problems affecting the rapid and healthy cultivation. Strengthening the immunity of Chinese soft-shelled turtles is extremely important to control the infection of pathogenic bacteria. Bacillus has attracted attention as a probiotic supplement in aquatic feeds.In our previous studies, we found that the addition of Bacillus subtilis B10 to diets could increase survival rate, daily weight gain (DG) and feed conversion ratio (FCR) of Chinese soft-shelled turtles, improving the activities of digestive enzyme and optimizing the microbial communities of intestinal in Chinese soft-shelled turtle.However, the study on the mechanism of Bacillus subtilis B10 in Chinese soft-shelled turtle culture remains rare. Therefore, in this study, we used Bacillus subtilis B10 to feed the turtle, and used RNA-seq to explore its mechanism.

2022-09-01 | GSE183769 | GEO

Screening and characterisation of sex differentiation-related long non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis).

Project description:Long non-coding RNAs (lncRNAs) perform distinct functions in various biological processes in mammals, including sex differentiation. However, the roles of lncRNAs in other vertebrates, especially in the Chinese soft-shell turtle (Pelodiscus sinensis), remain to be clarified. In this study, we performed genome-wide analysis of the lncRNA expression profiles in gonad tissues and screened numerous sex-specific lncRNAs in the Chinese soft-shell turtle. Of the 363,310,650 clean reads obtained, 5,994 sequences were typed as lncRNAs, of which 4,463 were novel. A selection of sex-specific lncRNAs (♀ 932, ♂ 449) from female ovaries and male testis were shown to act on target genes in cis and in trans, and most were involved in gonad differentiation based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Furthermore, interactions among the differentially expressed lncRNA-mRNAs and protein coding genes were identified by construction of correlation networks. Overall, our systematic analysis of lncRNA expression profiles in gonad tissues revealed numerous sex-specific lncRNAs in P. sinensis. Thereby, these findings provide new insights into the function of lncRNAs in sex differentiation and highlight a group of candidate lncRNAs for future studies.

| S-EPMC5988831 | biostudies-literature

Diversity of Underwater Vocalizations in Chinese Soft-Shelled Turtle (Pelodiscus sinensis)

Project description:Simple Summary Vocalization is important for the survival of underwater animals. Pelodiscus sinensis spends most of its life in water, and its wild population is highly vulnerable. However, its underwater vocalization, which can serve as the basis for ecological and evolutionary research, has not been explored. We identified 10 call types of the species from underwater recordings and found differences in vocalizations between individuals of different ages and sexes. The Chinese soft-shelled turtle has a high diversity of vocalizations and shows a tendency for vocalization to become more diverse with age. These features help them to adapt to complex and dark underwater environments. Abstract Sound communication is important for underwater species. The wild population of the Chinese soft-shelled turtle (Pelodiscus sinensis) is listed as vulnerable. However, its vocalization, which can serve as the basis for ecological and evolutionary research, has not been studied. Here, we performed underwater recordings of 23 Chinese soft-shelled turtles of different ages and sexes and identified 720 underwater calls. The turtle calls were manually divided into 10 call types according to visual and aural inspection properties. The similarity test indicated that the manual division was reliable. We described the acoustic properties of the calls and the statistical analysis showed that the peak frequency of calls was significantly different between adult females and males, and also between subadults and adults. Similar to other aquatic turtles that prefer to live in deep water, Chinese soft-shelled turtles have a high vocal diversity and many harmonic calls, indicating that this highly aquatic species developed a variety of vocalizations to enhance their underwater communication, which helped them adapt to the complex and dim underwater environment. Furthermore, the turtles showed a tendency for vocalization to become more diverse with age.

| S-EPMC10000088 | biostudies-literature

Project description:RNA methylaton of chinese soft-shell turtle

| PRJNA808173 | ENA

Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>).

Project description:In aquaculture, the Chinese soft-shelled turtle (Pelodiscus sinensis) is an economically important species with remarkable gender dimorphism in its growth patterns. However, the underlying molecular mechanisms of this phenomenon have not been elucidated well. Here, we conducted a whole-transcriptome analysis of the female and male gonads of P. sinensis. Overall, 7833 DE mRNAs, 619 DE lncRNAs, 231 DE circRNAs, and 520 DE miRNAs were identified. Some "star genes" associated with sex differentiation containing dmrt1, sox9, and foxl2 were identified. Additionally, some potential genes linked to sex differentiation, such as bmp2, ran, and sox3, were also isolated in P. sinensis. Functional analysis showed that the DE miRNAs and DE ncRNAs were enriched in the pathways related to sex differentiation, including ovarian steroidogenesis, the hippo signaling pathway, and the calcium signaling pathway. Remarkably, a lncRNA/circRNA-miRNA-mRNA interaction network was constructed, containing the key genes associated with sex differentiation, including fgf9, foxl3, and dmrta2. Collectively, we constructed a gender dimorphism profile of the female and male gonads of P. sinensis, profoundly contributing to the exploration of the major genes and potential ncRNAs involved in the sex differentiation of P. sinensis. More importantly, we highlighted the potential functions of ncRNAs for gene regulation during sex differentiation in P. sinensis as well as in other turtles.

| S-EPMC9219891 | biostudies-literature

Effects of dietary chito-oligosaccharide and β-glucan on the water environment and gut microbiota, intestinal morphology, immune response, and meat quality of Chinese soft-shell turtles (Pelodiscus sinensis)

Project description:Effects of dietary chito-oligosaccharide and β-glucan on the water environment and gut microbiota, intestinal morphology, immune response, and meat quality of Chinese soft-shell turtles (Pelodiscus sinensis)

| PRJEB65072 | ENA

| PRJEB65071 | ENA

Genome-wide identification, evolution and expression analysis of bone morphogenetic protein (BMP) gene family in chinese soft-shell turtle (<i>Pelodiscus sinensis</i>).

Project description:Introduction: Bone morphogenetic proteins (BMPs) play a crucial role in bone formation and differentiation. Recent RNA-Seq results suggest that BMPs may be involved in the sex differentiation of P. sinensis, yet more relevant studies about BMPs in P. sinensis are lacking. Methods: Herein, we identified BMP gene family members, analyzed the phylogeny, collinear relationship, scaffold localization, gene structures, protein structures, transcription factors and dimorphic expression by using bioinformatic methods based on genomic and transcriptomic data of P. sinensis. Meanwhile, qRT-PCR was used to verify the RNA-Seq results and initially explore the function of the BMPs in the sex differentiation of P. sinensis. Results: A total of 11 BMP genes were identified, 10 of which were localized to their respective genomic scaffolds. Phylogenetic analysis revealed that BMP genes were divided into eight subfamilies and shared similar motifs ("WII", "FPL", "TNHA", "CCVP", and "CGC") and domain (TGF-β superfamily). The results of the sexually dimorphic expression profile and qRT-PCR showed that Bmp2, Bmp3, Bmp15l, Bmp5, Bmp6 and Bmp8a were significantly upregulated in ovaries, while Bmp2lb, Bmp7, Bmp2bl and Bmp10 were remarkable upregulated in testes, suggesting that these genes may play a role in sex differentiation of P. sinensis. Discussion: Collectively, our comprehensive results enrich the basic date for studying the evolution and functions of BMP genes in P. sinensis.

| S-EPMC9928969 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data