Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabolic Roadmap to Nephrogenesis

ABSTRACT: CKD and hypertension to impact a staggering 1.5 billion individuals within the next decade. Optimal fetal growth and development are outcomes of a delicate interplay between genetic and environmental factors. Nutrition emerges as a pivotal environmental determinant, orchestrating proper organogenesis. Malnutrition disrupts normal embryo development and potentially leads to chronic diseases in later life. Our understanding of the specific metabolic routes and their impact on kidney development is still elusive. Here, we used a multi-omics approach to study the importance of glucose metabolism to proper kidney development. We cultured E13.5 embryonic kidneys in the presence or absence of partial inhibition of glycolysis and submitted it to transcriptomic and proteomic profiling. We found that glycolysis-derived acetyl-CoA is an intracellular pleiotropic agent pivotal for proper kidney development.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Kidney

SUBMITTER: Jennifer Klein

LAB HEAD: Giovane G Tortelote

PROVIDER: PXD045445 | Pride | 2023-09-18

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	04ZS_A_01.raw	Raw
	04ZS_A_02.raw	Raw
	04ZS_A_03.raw	Raw
	04ZS_A_04.raw	Raw
	04ZS_A_05.raw	Raw

Items per page:

1 - 5 of 39

Similar Datasets

NEUROMESO

Project description:Exposure of mouse ESCs to a sequence of extrinsic signals, which recapitulates in vivo development, generates a bipotential neuromesodermal precursor (NMP) that can be directed to differentiate into either spinal cord or paraxial mesodermal tissue. To induce differentiation,mouse ES cells were plated on CellBINDSurface dishes (Corning) precoated with 0.1% gelatin (Sigma) at a density of 5x10^3 cells cm-2 in N2B27 medium. Cells were grown in N2B27 supplemented with 10ng/ml bFGF (R&D) for 3 days (D1-D3) and then were transferred into serum free media without bFGF (D3-D5). To induce ventral hindbrain identity NPCs (NH) 100nM RA (Sigma) and 500nM SAG (Calbiochem) was added from D3-D5. Spinal cord identity (NP) was induced by the addition of 5nM CHIR 99021 (Axon) from D2 to D3 followed by 100nM RA, 500nM SAG from D3-D5. To induce mesodermal differentiation the cells were treated with CHIR99021 from D2-D5.

2014-07-18 | E-MTAB-2268 | biostudies-arrayexpress

m6A RNA Methylation is Critical for Adequate Exit from NaM-CM-/ve Pluripotency and Execution of Mammalian Development (m6a-seq)

Project description:In this study we identify Mettl3, an m6A RNA modification writer, as a critical regulator for terminating naM-CM-/ve pluripotency and a positive maintainer of primed pluripotency in vitro and in vivo. Remarkably, Mettl3 knockout pre-implantation epiblasts and naM-CM-/ve ES cells, entirely lack m6A on coding mRNAs and are viable. Yet, they fail to adequately terminate the naM-CM-/ve pluripotent state, and subsequently undergo aberrant priming and early lineage commitment at the post-implantation stage. A comprehensive functional and genomic analysis involving profiling of m6A, RNA transcription and translation in Mettl3 wild-type and knockout pluripotent and differentiated cells, identified m6A as a critical determinant that destabilizes secondary naM-CM-/ve specific pluripotency genes Esrrb, Klf4 and Nanog, and restrains their transcript stability and translation efficiency. In summary, our findings provide for the first time evidence for a critical role for an mRNA epigenetic modification in early mammalian development in vivo, and identify a mechanism that functionally regulates mouse naM-CM-/ve and primed pluripotency in an opposing manner. m6A-seq was measured from total RNA in mouse embryonic stem cells (ESCs), embroid bodies (EBs) and embronic fibroblasts (MEF). 3 biological replicates are available from BVSC ESC line and EBs, and two biological replicates are available for MEFs. Each sample consist of IP to m6A and control input

2014-11-02 | E-GEOD-61995 | biostudies-arrayexpress

m6A RNA Methylation is Critical for Adequate Exit from Naïve Pluripotency and Execution of Mammalian Development (RNA-Seq)

Project description:In this study we identify Mettl3, an m6A RNA modification writer, as a critical regulator for terminating naïve pluripotency and a positive maintainer of primed pluripotency in vitro and in vivo. Remarkably, Mettl3 knockout pre-implantation epiblasts and naïve ES cells, entirely lack m6A on coding mRNAs and are viable. Yet, they fail to adequately terminate the naïve pluripotent state, and subsequently undergo aberrant priming and early lineage commitment at the post-implantation stage. A comprehensive functional and genomic analysis involving profiling of m6A, RNA transcription and translation in Mettl3 wild-type and knockout pluripotent and differentiated cells, identified m6A as a critical determinant that destabilizes secondary naïve specific pluripotency genes Esrrb, Klf4 and Nanog, and restrains their transcript stability and translation efficiency. In summary, our findings provide for the first time evidence for a critical role for an mRNA epigenetic modification in early mammalian development in vivo, and identify a mechanism that functionally regulates mouse naïve and primed pluripotency in an opposing manner. polyA RNA-seq was measured in mouse embryonic stem cells (ESCs) and embroid bodies (EBs), each in WT and in Mettl3-KO cell lines. RNA-seq was measured also from WT mouse embronic fibroblasts (MEF). 3 biological replicates are available from ESCs and 2 from EBs. Replicate C in ESCs was measured alongside protein levels (SILAC) and was used for the analysis of that assay.

2014-11-02 | E-GEOD-61997 | biostudies-arrayexpress

scRNA-seq of Human Alveolar Type 2 Cell Organoids

Project description:Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in injury-repair. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development through differentiation of lung progenitor organoids to AT2 cells and benchmarking against primary AT2 organoids.

2023-06-15 | E-MTAB-12960 | biostudies-arrayexpress

Miz1 is required to maintain autophagic flux_2

Project description:To isolate neuronal progenitor cells (NPCs), forebrains of E13.5 Miz1+/+ or Miz1-delta-POZ embryos were cut in small pieces, digested with trypsin and filtered through sterile gauze. Cells were cultivated in 2:1 DMEM/F12 supplemented with 1xB27 (Life technologies), 20 ng/ul EGF (Biomol), 20 ng/?l basic FGF (Biomol), 1 ug/ml fungizone (Gibco) and Penicillin/Streptomycin (PAA). NPCs were passaged every seven days. RNA expression of different genotypes was compared in sec. and quart. neurospheres.

2013-10-01 | E-MEXP-3883 | biostudies-arrayexpress

Transcription profiling of embryonic kidneys from wild type and Hoxa11, Hoxd11 compound null mice throughout development to characterize Hoxa11/Hoxd11 mutant kidney development

Project description:Complete (whole) embryonic kidneys were dissected from wild type and Hoxa11, Hoxd11 compound null embryos throughout development. Targets from two biological replicates of each were generated and the expression profiles were determined using Affymetrix MOE430A and MOE430B arrays. Comparisons between normal and mutant and comparisons of development samples identified global patterns of gene regulation in kidney development Experiment Overall Design: Embryonic metanephric kidney samples throughout development were analyzed based on normalization to adult kidney samples. In addition, Hoxa11, Hoxd11 compound null embronic kidneys were normalized to wild type embryonic controls. All developmental and adult stages were represented in biological (seperate embryo/animal replicate).<br><br>Normalized data files were not included because there appears to be a mismatch between the composite sequence identifiers in some of them and the array design selected.

2008-10-15 | E-GEOD-3808 | biostudies-arrayexpress

Identification of differential expressed genes between P-RPCs, ESC-RPCs and Dkk1 treated ESC-RPCs through genome-wide transcript profiling

Project description:Tumor formation constitutes a major obstacle to the clinical application of embryonic stem cells (ESCs). As P-RPCs could successfully integrate into host eyes without development of teratomas or NOG, we sought to identify differentially expressed genes between P-RPCs and ESC-RPCs through genome-wide transcript profiling. Inhibition of Wnt signaling by DKK1 promotes the commitment of ESC-RPCs to more mature retinal cells and reduces the occurrence of NOG to 3%. DKK1-treated ESC-RPCs efficiently integrate to the host retina, form synaptic connections and restore visual function. Here, we report that further differentiation of ESC-derived neural progenitors into retinal progenitor cells (ESC-RPCs) completely eliminates teratomas in ocular transplantation. However, tumor-like neural overgrowth (NOG) occurs in 61% of transplanted eyes. ESC-RPCs were divided into two groups according to the differentiation stages for RNA extraction and hybridization on Affymetrix microarrays. Normal control ESC-RPCs (N) were represented the homogeneous populations of early stage expression profiles of immature ESC-RPCs. DKK1 treated ESC-RPCs (D) were represented the homogeneous populations of late stage expression profiles of further differetiated mature ESC-RPCs. To sought the pathways involved in the proliferation and oncogenesis of ESC-RPCs, the newborn C57 mice reitinal progenitor cells (R) were applied as negative control. Each group above had three independent biological repeats.

2013-04-16 | E-GEOD-34002 | biostudies-arrayexpress

Role of 14-3-3ζ in the adipogenesis program and the differentiation of healthy adipose tissue

Project description:Obesity is an independent risk factor for diabetes and cardiovascular disease. Before effective anti-obesity therapies can be developed, understanding of what governs the production of healthy versus unhealthy fat tissue is required, as not all types confer equal risk. Adipogenesis requires the precise transduction of signals and coordination of transcription factor cascades. Molecular adaptor proteins of the 14-3-3 family are known to coordinate signaling events from multiple cues, but whether specific isoforms have unique, non-redundant roles in adipogenesis remains unclear. RNAi screening revealed 14-3-3ζ as the critical isoform for in vitro adipocyte differentiation. This study aims to understand the role of 14-3-3ζ in adipogenesis program and the differentiation in health adipose tissue.

2022-03-01 | PXD001215 | Pride

The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways

Project description:Generation of oligodendrocytes (OLs) is a sophisticated multistep process, mechanistic underpinnings of which are not fully understood and demand further investigation. To systematically profile proteome dynamics during human embryonic stem cell (hESC) differentiation into OLs, we applied in-depth quantitative proteomics at different developmental stages and monitored changes in protein abundance using a multiplexed tandem mass tag (TMT) based proteomics approach. Findings: Our proteome data provided a comprehensive protein expression profile that highlighted specific expression clusters based on the protein abundances over the course of human OL lineage differentiation. The proteome profile of OL lineage cells revealed 378 proteins that were specifically up-regulated only in one differentiation stage. In addition, comparative pairwise analysis of differentiation stages demonstrated that abundances of 352 proteins differentially changed between consecutive differentiation time points. Our results highlighted the eminence of the planar cell polarity (PCP) signaling and autophagy (particularly macroautophagy) in the progression of OL lineage differentiation

2020-09-16 | PXD017649 | Pride

Induction of pluripotency in human somatic cells via a primitive streak-like state

Project description:During mammalian embryonic development, the primitive streak is initiates the differentiation of pluripotent epiblast cells into germ layers. Pluripotency can be reacquired in committed somatic cells using a combination of handful transcription factors, such as OCT3/4, SOX2, KLF4 and c-MYC (hereafter referred to as OSKM), albeit with low efficiency . Here we show that, during the OSKM-induced reprogramming process toward pluripotency in human cells, intermediate cells transiently show gene expression profiles resembling mesendoderm, which is a major component of the primitive streak. Based on these findings, we discover that forkhead box H1 (FOXH1), a transcription factor required for anterior primitive streak specification during early development, significantly enhances the reprogramming efficiency of human fibroblasts by promoting their maturation, including the mesenchymal to epithelial transition and the activation of late pluripotent markers. These results demonstrate that during the reprogramming process, human somatic cells go through a transient state that resembles mesendoderm. Human differentiated progeny derived from pluripotent stem cells, N=13 Human undifferentiated pluripotent stem cells, N=6 Transgenic ESC line, N=6 Human tissues, N=29 Human tissue-derived cells, N=20 Human nascent reprogrammed cells, N=95 Mouse cells, N=12

2014-04-24 | E-GEOD-50206 | 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