Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative RNA-seq analysis between control and SU5402 treated amphioxus (Branchiostoma lanceolatum) embryos

ABSTRACT: We compared the transcriptomes of Amphioxus (Branchiostoma lanceolatum) control and SU5402 treated embryos to define putative FGF signalling pathway target genes during somitogenesis. Embryos were treated with 50µM of SU5402 from 5.5hpf to 8.5hpf, 11.5hpf, and 14.5hpf or from 15hpf to 18hpf, 21hpf, 24hpf. Total RNA was extracted from control and treated embryos.

ORGANISM(S): Branchiostoma lanceolatum

PROVIDER: GSE122245 | GEO | 2020/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Comparative RNA-seq analysis between control and SU5402 treated amphioxus (Branchiostoma lanceolatum) embryos

Project description:Comparative RNA-seq analysis between control and SU5402 treated amphioxus (Branchiostoma lanceolatum) embryos

| PRJNA504393 | ENA

microRNA expression changes after lipopolysaccharide treatment in gills of amphioxus Branchiostoma belcheri

Project description:Recently, amphioxus has served as a model for studying the origin and evolution of vertebrate immunity. However, little is known about how microRNAs (miRNAs) are involved in the immune defense in amphioxus. In this article, we identified the amphioxus miRNAs in the acute-phase response to Lipopolysaccharide (LPS). First, we determined the time point for the peak of immune response in amphioxus after LPS challenge by evaluating the expression of TLR4 and NF-κb(v-rel) which were commonly used immune response indicators. Then we performed miRNA microarray analysis on gill samples collected at the time point to select the differentially expressed miRNAs. Finally, we used real-time quantitative PCR to detect the expression patterns of amphioxus miRNAs under effective LPS challenge during the time course. The microarray data revealed that the miRNA expression file was significantly changed after LPS stimulation. The changes of the most upregulated and most downregualted miRNAs in gills of the amphioxus following challenge with LPS revealed a temporal induction kinetic. Our current study will provide valuable information to take an insight into molecular mechanism of innate immune and the evolution of the miRNA family.

2017-03-10 | GSE85326 | GEO

Solexa sequencing of small RNAs in Chinese Amphioxus

Project description:We applied Solexa sequencing technology to identify Amphioxus microRNA genes. We identified 113 amphioxus microRNA genes, 55 were conserved across species and coded for 45 nonredundant mature miRNAs, whereas 58 were amphioxus-specific and accounted for 53 mature miRNAs. Analyzing the evolutionary history of amphioxus miRNAs, we found amphioxus possessed many miRNAs that are also found in chordates and vertebrates, suggesting these miRNAs may represent cephalochordate lineage innovation. By detailed comparison of the miRNA phylogenetic histories, we further found that amphioxus is more vertebrate-like than tunicates. Keywords: Small RNA 18-30 nt small RNAs from 12 adult Chinese Amphioxus were sequenced in one Solexa lane.

2009-06-29 | E-GEOD-16859 | biostudies-arrayexpress

Solexa sequencing of small RNAs in Chinese Amphioxus

2009-06-30 | GSE16859 | GEO

Transcription profile of hearts extracted from zebrafish embryos treated with SU5402 at 48 hpf

Project description:Heart formation requires input from two populations of progenitor cells - the first and second heart fields - that differentiate at distinct times and create different cardiac components. The cardiac outflow tract (OFT) is built through recruitment of late-differentiating, second heart field (SHF) -derived cardiomyocytes to the arterial pole of the heart. Mechanisms responsible for selection of an appropriate number of OFT cells from the SHF remain unclear, although several lines of evidence emphasize the importance of FGF signaling in promoting this process. Here, we examine the impact of inhibition of FGF signaling on cardiac transcription profiles in an effort to identify genes operating downstream of FGF during OFT development. We compared hearts from embryos treated with the FGFR inhibitor SU5402 to the hearts from sibling embryos treated with DMSO. Two replicates were performed.

2014-05-12 | E-GEOD-55540 | biostudies-arrayexpress

Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud

Project description:We aimed to expand the knowledge of Fgf and Wnt signaling in the zebrafish tailbud. Both pathways are required for proper axis elongation and segmentation and we wished to explore the genes under the control of each pathway during this process. In addition, we saught to identify crosstalk between the two pathways by determining whether pathway effector expression was being changed after time-resolved modification of each pathway using pharmacological modifiers. Embryos were treated with either 0.3M LiCl, 50uM SU5402, or E2 for 3hours or 7 hours (E2 and SU5402), followed by tailbud dissection and RNA extraction. Conditions were replicated in triplicate.

2012-07-15 | E-GEOD-38969 | biostudies-arrayexpress

Phagocytic intracellular digestion in amphioxus (Branchiostoma).

Project description: Not available

| S-EPMC6015868 | biostudies-literature

A single 3D chromatin compartment in amphioxus Hox cluster suggests a stepwise evolutionary origin for vertebrate Hox bimodal regulatory topologies

Project description:Comparison among vertebrates and the cephalochordate amphioxus Hox clusters architectures 4C-seq experiments from promoters spanning the amphioxus Hox cluster and the zebrafish hoxd cluster and surrounnding areas,

2015-12-16 | E-GEOD-68737 | biostudies-arrayexpress

Differential Roles of the Maternal and Zygotic FGF in Neural Induction in the Zebrafish Embryo

Project description:Comparison of ATAC-seq and RNA-seq datasets in wild type and SU5402 treated zebrafish embryos

2019-11-29 | GSE90637 | GEO

ATAC-seq data of control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.

Project description:The goal of this projet was to identify genomic region showing differential accessibility between control and Activin-treated amphioxus explants at two time points (gastrula and neurula stage)

2022-01-24 | GSE166495 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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