Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mechanical force induces rapid phosphorylation-dependent signaling in Xenopus embryos

ABSTRACT: We inegrated quantitative phosphoproteome, proteome, a tergeted MS analysis, in conjunction with pathway perturbation to obtain a global view of the mechano-responses of embryonic tissues. This study provides mechanistic insights into mechanical force sensing pathways.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Xenopus Laevis (african Clawed Frog)

TISSUE(S): Embryo

SUBMITTER: Yutaka Hashimoto

LAB HEAD: Ileana M. Cristea

PROVIDER: PXD010676 | Pride | 2019-02-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	170728_phospho_time0_01.msf	Msf
	170728_phospho_time0_01.raw	Raw
	170728_phospho_time0_02.msf	Msf
	170728_phospho_time0_02.raw	Raw
	170728_phospho_time0_03.msf	Msf

Items per page:

1 - 5 of 78

Similar Datasets

Mechanical force induces rapid phosphorylation-dependent signaling in Xenopus embryos

Project description:We inegrated quantitative phosphoproteome, proteome, a tergeted MS analysis, in conjunction with pathway perturbation to obtain a global view of the mechano-responses of embryonic tissues. This study provides mechanistic insights into mechanical force sensing pathways.

2019-10-09 | MSV000084444 | MassIVE

Cardiac transcriptome of Tcf21-depleted Xenopus embryos

Project description:The aim of the approach was to use RNAseq analysis to identify genes expressed in Xenopus epicardium that were affected by embryonic depletion of the epicardial transcription factor Tcf21 compared to control-MO injected siblings. Both upregulated and downregulated genes were validated by RT-PCR and whole embryo in situ hybridization to validate gene expression and assess spatio-temporal distribution of genes of interest within the heart and epicardium. Approximately 70-100 stage 44-46 Xenopus laevis hearts were dissected to isolate total mRNA from which poly-adenylated RNA was extracted using the Illumina standard protocol. This experiment represents one replicate from pooled hearts. mRNA profiles of stage 44-45 Xenopus laevis sibling hearts from control or Tcf21-depleted embryos, were generated by deep sequencing using Illumina GAII.

2013-07-05 | E-GEOD-45786 | biostudies-arrayexpress

Histone modification and transcription factor ChIPseq of Xenopus laevis epithelial progenitors

Project description:To determine the positions of promoters and enhancers in developing Xenopus laevis epithelial progenitors, we performed ChIPseq on the histone modifications H3K4me3 and H3K27ac. We also performed ChIPseq on the transcription factors foxj1 (in the presence or absence of rfx2), myb (in the presence or absence of multicilin), and rad21. Some embryos were harvested as wild-types; in other experiments, we injected embryos with mRNAs encoding FLAG-foxj1 (with and without rfx2 morpholino) or GFP-myb (with and without an inducible form of multicilin (mcidas-HGR)). We then isolated epithelial progenitors surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed ChIPseq using antibodies against endogenous targets (H3K4me3, H3K27ac, rad21) or protein tags (FLAG, GFP). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1) with bwa mem and called peaks with HOMER, using input as background.

2016-02-23 | E-GEOD-78176 | biostudies-arrayexpress

Xenopus Hwa IP-MS in 1 cell stage embryos

Project description:Spemann and Mangold Organizer (SMO) is of fundamental importance for the dorsal ventral body axis formation during vertebrate embryogenesis. Maternal Huluwa (Hwa) has been identified as the dorsal determinant that is both necessary and sufficient for the SMO formation. However, it remains unclear how Hwa is regulated. Here we report that the E3 ubiquitin ligase zinc and ring finger 3 (ZNRF3) is essential for restricting the spatial activity of Hwa, and therefore the proper SMO formation in Xenopus leavis. ZNRF3 interacts with and ubiquitinates Hwa thereby regulating its lysosomal trafficking and protein stability. Perturbation of ZNRF3 leads to the accumulation of Hwa and induction of ectopic axis in embryos. Ectopic expression of ZNRF3 promotes Hwa degradation and damps the axis-inducing activity of Hwa. Thus, our findings identify a substrate of ZNRF3, but also highlight the importance of the regulation of Hwa temporospatial activity in body axis formation in vertebrate embryos.

2021-09-29 | PXD027207 | Pride

Identification of microRNAs and microRNA targets in Xenopus ectoderm

Project description:Purpose: The establishment of cell lineages occurs via a dynamic progression of gene regulatory networks that underlie developmental commitment and differentiation. To investigate how microRNAs (miRs) function in this process, we compared miRs and miR targets at the initiation of the two major ectodermal lineages in Xenopus. Methods: We injected Xenopus laevis embryos with noggin or constitutively active BMP4 receptor (CABR) at two-cell stage and cut animal caps at stg. 8. Isolated animal caps were grown separately till mid gastrula and processed for either RNA isolation or immunoprecipitation. Results: We have identified over 400 miRNAs in early neural and epidermal ectoderm. The Ago-RNP RNAs from these tissues represent overlapping, yet distinct, subsets of genes. Moreover, the profile of Ago-RNP associated genes differs substantially from the profile of total RNAs in these tissues. Identification of microRNAs and microRNA targets in establishment of early ectodermal tissues in Xenopus.

2016-06-28 | E-GEOD-83784 | biostudies-arrayexpress

Mechanical Force Induces Phosphorylation-Mediated Signaling that Underlies Tissue Response and Robustness in Xenopus Embryos.

Project description:Mechanical forces are essential drivers of numerous biological processes, notably during development. Although it is well recognized that cells sense and adapt to mechanical forces, the signal transduction pathways that underlie mechanosensing have remained elusive. Here, we investigate the impact of mechanical centrifugation force on phosphorylation-mediated signaling in Xenopus embryos. By monitoring temporal phosphoproteome and proteome alterations in response to force, we discover and validate elevated phosphorylation on focal adhesion and tight junction components, leading to several mechanistic insights into mechanosensing and tissue restoration. First, we determine changes in kinase activity profiles during mechanoresponse, identifying the activation of basophilic kinases. Pathway interrogation using kinase inhibitor treatment uncovers a crosstalk between the focal adhesion kinase (FAK) and protein kinase C (PKC) in mechanoresponse. Second, we find LIM domain 7 protein (Lmo7) as upregulated upon centrifugation, contributing to mechanoresponse. Third, we discover that mechanical compression force induces a mesenchymal-to-epithelial transition (MET)-like phenotype.

| S-EPMC6453581 | biostudies-literature

Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

Project description:Recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells. In contrast, single cell proteomics analyses have been restricted to targeted analyses, for example using flow cytometry with GFP fusions or mass cytometry. Here, we performed global absolute protein quantification of single Xenopus laevis eggs using mass spectrometry-based proteomics. We quantified over 5800 proteins, thus representing the largest single cell proteome that has been characterized to date. Absolute protein amounts in single eggs are highly comparable, thus indicating a tight regulation of global protein abundance. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identified 439 proteins that significantly change in abundance during early embryogenesis. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in Xenopus leavis eggs. RNA-seq in Xenopus laevis of 5 replicates of both single eggs and single embryos.

2014-08-04 | E-GEOD-56586 | biostudies-arrayexpress

Xenopus laevis kidney-induced animal caps nanoLC-MS/MS - Xenopus Ssbp2 is required for embryonic pronephros morphogenesis and terminal differentiation.

Project description:The nephron, functional unit of the vertebrate kidney, is specialized in metabolic wastes excretion and body fluids osmoregulation. Given the high evolutionary conservation of gene expression and segmentation patterning between mammalian and amphibian nephrons, the Xenopus laevis pronephric kidney offers a simplified model for studying nephrogenesis. The Lhx1 transcription factor plays critical roles in kidney development, regulating target gene expression by forming multiprotein complexes with LIM binding protein 1 (Ldb1). However, few Lhx1-Ldb1 cofactors have been identified for this organ formation. By tandem- affinity purification from kidney-induced Xenopus animal caps, we identified single-stranded DNA binding protein 2 (Ssbp2) to interact with the Ldb1-Lhx1 complex. Ssbp2 is expressed in the Xenopus pronephros, and knockdown prevents normal morphogenesis and differentiation of the glomus and the convoluted renal tubules. We demonstrate a role for a member of the Ssbp family in kidney organogenesis and provide evidence of a fundamental function for the Ldb1-Lhx1-Ssbp transcriptional complexes in embryonic development.

2023-10-24 | PXD041761 | Pride

Xenopus A6 cells nanoLC-MS/MS - The Lhx1-Ldb1 complex interacts with Furry to regulate microRNA expression during pronephric kidney development

Project description:The transcriptional events driving specification of the kidney have been well characterized. However, it remains undetermined how initial kidney field size is established, patterned, and proportioned. Lhx1 is a transcription factor expressed in the kidney anlage and is required for specification of the kidney field, but few Lhx1 interacting cofactors or downstream targets have been identified. By tandem-affinity purification, we isolated Furry (FRY), a multifunctional protein that acts as a transcriptional co-repressor of microRNAs. We found that Xenopus embryos depleted of fry exhibit loss of the kidney field, phenocopying the lhx1 depleted animals. In addition, we demonstrated synergism between Fry and Lhx1, identified candidate microRNAs regulated by the pair, and confirmed these microRNA clusters influence specification of the kidney field. Therefore, our data shows that a tissue-specific transcription factor, Lhx1, interacts with a broadly expressed microRNA repressor, Fry, to establish the kidney field.

2019-11-11 | PXD006926 | Pride

LC-MSMS of DCC and Neuropilin-1 immunoprecipitated samples from Xenopus Laevis brains

Project description:During neuronal wiring, extrinsic cues trigger the local translation of specific mRNAs in axons via cell surface receptors. The coupling of ribosomes to receptors has been proposed as a mechanism linking signals to local translation but it is not known how broadly this mechanism operates, nor whether it can selectively regulate mRNA translation. Here, we analyzed the interactome of endogenous DCC and Neuropilin-1 by analysing immunoprecipitated samples obtained from Xenopus Laevis brains with LC-MSMS. We find that DCC and Neuropilin-1 bind to ribosomal proteins and specific RNA-binding proteins confirming that multiple guidance cue receptors can bind to ribosomes and may use receptor-ribosome coupling to regulate cue-induced local translation in axons.

2019-12-02 | PXD015650 | Pride

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