Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of testis Transcriptomes in Xenopus laevis

ABSTRACT: Purpose: Circular RNAs (circRNAs) are implicated in multiple developmental anomalies. The goals of this study are to research whether circRNAs involve in the effects in atrazine (AZ)-exposed X. laevis Methods: At Nieuwkoop-Faber (NF) stage 47 (13 d post-hatch), mixed sex X. laevis tadpoles exposed to 100 µg/L AZ for 180 days. Then total RNAs from individual testis was isolated. RNA library construction and circRNA sequencing was analysis Results: CircRNAs were detected and identified with Find_circ software. We found that treatment of AZ led to 405 circRNAs differentially expressed including 44 upregulated and 361 downregulated compared with froglets in the control groups. Two hundreds and eighty two differentially expressed circRNAs played miRNA sponges roles. Kyoto Encyclopedia of Genes and Genomes pathway analysis of miRNA targets showed that AZ-affected circRNAs are mainly involved in 19 pathways Conclusions: This study for the fisrt time provides evidence that AZ can alter circRNAs which play a role in AZ-induced testicular degeneration of developing male X. laevis through regulation of expressions of functional genes in the testes of X. laevis.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE103526 | GEO | 2019/09/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome sequencing of Xenopus laevis animal caps at six time points in transit from pluripotency to 4 lineages: epidermal, neural, ventral mesoderm and endoderm

Project description:The purpose of this study is to examine transciptome dynamics at high resolution to 4 separate lineages. Here we provide snapshots of the Xenopus laevis transcriptome at Nieuwkoop and Faber stages 9., 10, 10.5, 11, 12 and 13 for the epidmeral, neural, ventral mesoderm and endoderm lineage

2022-10-23 | GSE198598 | GEO

Gene expression in sexually differentiating gonads of Xenopus laevis

Project description:The aim of this study was to study the gene expression profile in developing female and male gonads of Xenopus laevis at four stages: at the Nieuwkoop-Faber stage 50 (genital ridge), at NF53 (sex-determining period), NF56 (the onset of sexual differentiation), NF62 (gonads sexually differentiated).

2017-10-18 | GSE105103 | GEO

The effects of simazine, a chlorotriazine herbicide, on expression of genes in developing male Xenopus laevis

Project description:Numerous studies have shown simazine produces adverse effects on growth, development, immune and endocrine system functions in a wide range of species, few describe gene expression changes concurrent with simazine-induced changes in phenotype during development. In this report, developing Xenopus laevis tadpoles were chronically exposed to simazine for 90 days at dosages of 0.1, 1, 10 and 100µg/L. Affymetrix microarrays and Taqman RT-PCR were used to define gene expression changes in male tadpoles exposed to 100µg/L atrazine.

2014-12-30 | GSE64534 | GEO

Differential expression analysis of Gcn5 knockdown embryos at early developmental stage 10.5 in Xenopus laevis

Project description:We sequenced cDNA prepared from ribosomal RNA depleted total RNA of 10-10 embryos injected with Gcn5-antisense oligonucleotides and with water to create expression profiles of Gcn5 knockdown and control, respectively, in Xenopus laevis at early embryonic developmental stage 10.5. (according to Nieuwkoop and Faber), and we executed differential expression analysis of sequence count data (DEseq).

2016-03-07 | GSE76991 | GEO

Differential expression analysis of triple knockdown of TBP and TBP-related factors (TKD) in Xenopus laevis embryos at early developmental stage 10.5

Project description:We sequenced cDNA prepared from ribosomal RNA depleted total RNA of 10-10 embryos co-injected with TBP-,TBP2- and TLF-AS antisense oligonucleotides and with water to create expression profiles of triple knockdown of TBP/TBP-related factors (TKD) and control, respectively, in Xenopus laevis at early developmental stage 10.5. (according to Nieuwkoop and Faber). We executed differential expression analysis of sequence count data (DEseq).

2016-03-07 | GSE76994 | GEO

Expression data from Xenopus embryos treated with TTNPB (RAR-agonist), AGN193109 (RAR-antagonist), or Control Vehicle

Project description:Percellome analysis of whole Xenopus embryos at developmental stage 18 Xenopus embryos were treated with TTNPB (RAR-agonist), AGN193109 (RAR-antagonist), or Control Vehicle at Nieuwkoop and Faber Stage 7. Embryos were collected at stage 18, followed by RNA extraction, hybridization on Affymetrix microarrays, and Percellome analysis.

2014-05-06 | E-GEOD-57352 | biostudies-arrayexpress

Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans: atrazine

Project description:Physiologically based modelling using DEBtox (dynamic energy budget in toxicology) and transcriptional profiling were used in Caenorhabditis elegans to identify how physiological modes of action, as indicated by effects on system level resource allocation were associated with changes in gene expression following exposure to atrazine (AZ). For AZ, the physiological mode of action predicted by DEBtox was increased cost for maintenance. The transcriptional analysis demonstrated that this increase resulted from effects on DNA integrity as indicated by changes in the expression of genes chromosomal repair. Our results have established that outputs from process based models and transcriptomics analyses can help to link mechanisms of action of toxic chemicals with resulting demographic effects. Such complimentary analyses can assist in the categorisation of chemicals for risk assessment purposes. Adults of C. elegans strain GE-31 exposed as biological replicate groups (approx 10,000) to a control and 4 concentrations of atrazine from L1 stage. Replicate populations were sampled 12 hours after the on-set of egg laying and hybridised against a common reference for purposes of normalisation. All experiments were conducted following a reference design with the reference sample compiled from a mixture of RNA extracted from control and cadmium-, fluoranthene-, atrazine- and copper-exposed worms from L1, L4 and adult life-stages. Use of this reference was intended to provide optimal coverage of the spotted genes.

2010-03-23 | E-GEOD-21008 | biostudies-arrayexpress

A mixture of chemicals found in human amniotic fluid disrupts brain gene expression and behavior in Xenopus laevis

Project description:We hypothesized that embryonic exposure to a mixture of chemicals (containing phenols, phthalates, pesticides, heavy metals, and perfluorinated, polychlorinated, and polybrominated compounds) identified as commonly found in the human amniotic fluid (as calculated in Fini et al., ) could lead to altered brain development. We assessed its effect on TH signaling and neuro-development in an amphibian model (Xenopus laevis) highly sensitive to thyroid disruption. Fertilized eggs were exposed for eight days to either TH (thyroxine, T4 10 nM) or the amniotic mixture (at the actual concentration) until reaching stage NF47, where we analyzed gene expres-sion in the brains of exposed tadpoles using both RT-qPCR and RNA sequencing.

2023-01-27 | GSE223829 | GEO

Single cell RNA-seq of limb tissue from regeneration-competent, -restricted and -incompetent Xenopus laevis tadpoles

Project description:Xenopus laevis tadpoles display a decreasing capacity to regenerate their limbs following injury according to developmental stage. By comparing the regenerative response during the naturally occurring regeneration-competent, -restricted and -incompetent stages, scRNAseq can reveal cell type changes that are required for successful regeneration.

2021-05-17 | E-MTAB-9104 | biostudies-arrayexpress

Single cell RNA-seq of tail tissue from regeneration-competent and -incompetent Xenopus laevis tadpoles

Project description:Xenopus laevis tadpoles differ in their regenerative potential according to their developmental stage. Here, we focus on tail regeneration following amputation. By comparing the regenerative response during the naturally occurring regeneration-competent and -incompetent stages, scRNAseq can reveal cell type changes that are required for successful regeneration.

2019-04-23 | E-MTAB-7716 | biostudies-arrayexpress

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