Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

56 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell sequencing of renal endothelial cell heterogeneity and metabolic transcriptome adaptation to dehydration.

ABSTRACT: Renal endothelial cells (RECs) from glomerular cortical and medullary kidney compartments are exposed to different microenvironmental conditions. Upon dehydration medullary RECs (mRECs) are exposed to extreme hyperosmolarity. However the heterogeneous phenotypes of RECs remain in-completely inventoried and how mRECs respond to dehydration is unknown. By single cell RNA-sequencing of >40000 RECs we identified 24 (including 8 novel) REC phenotypes highlighting extensive heterogeneity of RECs between and within the cortex glomeruli and medulla. In response to dehydration mRECs upregulated primarily the expression of genes involved in the hypoxia response glycolysis and surprisingly oxidative phosphorylation (OXPHOS). In vitro mRECs increased oxygen consumption in response to hyperosmolarity presumably to sustain ATP production for Na+/K+ ATPase pump-mediated salt excretion and to generate metabolic water during OXPHOS in order to counteract mREC hyperosmolarity unveiling a previously underappreciated role of OXPHOS. Overall RECs exhibit extensive heterogeneity and plasticity to adapt their metabolic transcriptome to overcome dehydration.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Shawez Khan

PROVIDER: E-MTAB-8145 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Proteomic Profiling of Brain and Medullar Reveals the Dysregulation of Myosin Complex and Striated Muscle Contraction Pathway in ALS mouse model

Project description:In this study, we used this strategy to reveal the proteome changes of cerebral cortex, hippocampus and medulla of SOD1*G93A mice. Hundreds of changed proteins and many of important biological process were found in the ALS mouse brain.

2019-03-21 | PXD010553 | Pride

Expression data from renal dendritic cells under homeostatic conditions and from donor and host dendritic cells from renal allografts (3 days post-transplantation), isolated from cortex and medulla.

Project description:Renal dendritic cells play key roles in renal homeostasis and during kidney allograft rejection. Microarray analysis aims to evaluate whether dendritic cells modulate their gene expression profile in relation to their distribution in the different renal compartments (with varying biophysical characteristics), under homeostatic conditions and during acute renal allograft rejection (3 days post-transplantation). Renal dendritic cells from homeostatic (healthy) kidneys and donor/host dendritic cells from renal allografts (3 days post-kidney transplantation) were isolated from cortex and medulla, through fluorescence-activated cell sorting (FACS). Total RNA was isolated from FACS-sorted cells and amplified. The cDNA product was fragmented, biotin-labeled and hybridized on Affimetrix arrays.

2015-02-04 | E-GEOD-65564 | biostudies-arrayexpress

rat kidney LC-MS - Exploring the Therapeutic Mechanism of Desmodium styracifolium on Oxalate Crystal-Induced Kidney Injuries Using Comprehensive Approaches Based on Proteomics and Network Pharmacology

Project description:Oxalate-induced kidney injury rat model were established.The differentially expressed proteins in the kidneys between the oxalate and control groups were explored.

2018-10-19 | PXD009496 | Pride

The effect of cortex/medulla proportions on molecular diagnoses in kidney transplant biopsies: rejection and injury can be assessed in medulla

Project description:Histologic assessment of kidney transplant biopsies relies on cortex rather than medulla, but for microarray studies, the proportion cortex in a biopsy is typically unknown and could affect the molecular readings. The present study aimed to develop a molecular estimate of proportion cortex in biopsies and examine its effect on molecular diagnoses. Microarrays from 26 kidney transplant biopsies divided into cortex and medulla components and processed separately showed that many of the most significant differences were in glomerular genes e.g. NPHS2, NPHS1, CLIC5, PTPRO, PLA2R1, PLCE1, PODXL and REN. Using NPHS2 (podocin) to estimate proportion cortex, we examined whether proportion cortex influenced molecular assessment in the Molecular Microscope Diagnostic System. In 1190 unselected kidney transplant indication biopsies (Clinicaltrials.govNCT01299168), only 11% had <50% cortex. Molecular scores for ABMR, TCMR, and injury were independent of proportion cortex. Rejection was diagnosed in many biopsies that were mostly or all medulla. Agreement in molecular diagnoses in paired cortex/medulla samples (23/26) was similar to biological replicates (32/37). We conclude that NPHS2 expression can estimate proportion cortex; that proportion cortex has little influence on molecular diagnosis of rejection, and that, although histology cannot assess medulla, rejection does occur in medulla as well as cortex. We studied 26 pairs of cortex/medulla biopsies from 26 patients (4 unpaired), characterizing the clinical and histological features, and defined the mRNA phenotype with Affymetrix expression microarrays. We also studied 37 pairs of biopsies from biological replicates and 12 pairs from technical replicates. This dataset is part of the TransQST collection.

2017-04-27 | E-GEOD-95611 | biostudies-arrayexpress

Gene expression analysis of rat glomerular parietal epithelial cells

Project description:Very little is known about the function of glomerular parietal epithelial cells (PECs). In this study, we performed genome-wide expression analysis on PEC-enriched capsulated vs. PEC-deprived decapsulated rat glomeruli to determine the transcriptional state of PECs under normal conditions. We identified hundreds of differentially expressed genes that mapped to distinct biologic modules including development, tight junction, ion transport, and metabolic processes. Since developmental programs were highly enriched in PECs, we characterized several of their candidate members at the protein level. Collectively, our findings confirm that PECs are multifaceted cells and help define their diverse functional repertoire. We developed a sequential sieving methodology to selectively isolate capsulated (PEC-enriched) glomeruli from un-capsulated (PEC-deprived) glomeruli in rats. Three samples were obtained for each preparation. Total RNA was isolated and its integrity confirmed via Bioanalyzer 2100. Each sample (n =6) was hybridized to an Affymetrix Rat GeneChip 1.0ST microarray.

2014-08-01 | E-GEOD-54085 | biostudies-arrayexpress

scRNA-seq of human fetal lung primary tissues and cell cultures derived from fetal bud tip progenitors under dual SMAD treatment

Project description:Underdeveloped lungs are a primary cause of morbidity and mortality in premature infants, but our ability to help these patients by speeding up lung development are hindered by a lack of understanding of human lung developmental biology. Here, we performed single cell RNA sequencing of the human fetal lung from samples spanning from 11.5 weeks gestation to 21 weeks gestation from the distal lung, middle airways, and the tracheal epithelium. The primary goal of this experiment was to define fetal cell states to serve as a gold standard for pluripotent stem cell-derived lung cells and tissues, and to identify potential signaling pathways that drive differentiation of lung progenitor cells to mature cell types. Additionally, we generated bud tip progenitor organoids from 12 week human fetal lung bud tip progenitors. We show that treatment of bud tip progenitor organoids with a short pulse of dual SMAD activation (BMP4+TGFb1) led to the upregulation of lung basal cell markers, a cell type that serves as a critical stem cell for the adult airway, and that further treatment with dual SMAD inhibition leads to the generation of airway-like organoids containing differentiated cell types of the adult airway, including basal stem cells.

2020-04-17 | E-MTAB-8221 | biostudies-arrayexpress

Proteomic study of low-birth-weight nephropathy molecular pathogenesis in rats

Project description:We investigated the molecular pathogenesis of LBW rats obtained by intraperitoneal injection of dexamethasone into pregnant animals. Normal-birth-weight (NBW) rats were used as controls with seven animals per group. When the rats were four weeks old, the left kidneys were removed and used for comprehensive label-free proteomic studies

2022-02-15 | PXD018948 | Pride

Expression profiling of genes involved in somatic and zygotic embryo development in cotton

Project description:We used a next-generation sequencing approach, Illumina Digital Gene Expression II (DGEII) technology, to Genome-wide profiling of gene expression during somatic (SE) and zygotic embryo (ZE) development. As a result, 4242 differentially expressed genes (DEGs) were identified between SE and ZE. Expression pattern cluster and functional classification analysis of the differentially expressed genes revealed that large number of genes indicative of response to stress highly expressed in somatic embryos. Combined with KEGG analysis and BLAST annotation, genes related to stress response in DEGs have been comprehensively analyzed, mainly including: ABA biosynthesis, ABA and JA (jasmonic acid) response, LEA (late embryogenesis abundant protein) family members, RD (responsive to dehydration) and ERD (early responsive to dehydration) family members, Hot Shock Proteins, WRKY family members and NAC family members. Semi-quantitative Reverse Transcriptase-PCR (RT-PCR) analysis was performed on 27 selected genes and and the results enhance that genes related to stress response were involved in SE development. Our main goal is to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. This is a systematical expression analysis focusing on somatic embryo development, and also a global comparison between somatic and zygotic embryo at transcript level. Therefore, this study might bring new insights into the regulation of somatic embryo development. An analysis of differentially expressed genes at 3 parallel stages during somatic and zygotic embryo development in cotton by next-generation sequencing, using Illumina Digital Gene Expression II (DGE II) .

2013-09-27 | E-GEOD-45671 | biostudies-arrayexpress

Molecular fingerprint of the podocyte reveals novel gene regulatory networks

Project description:The thorough characterization of the transcriptome of endogenous podocytes has been hampered by low yields of cell isolation procedures. Here we introduce a double fluorescent reporter mouse model combined with an optimized bead perfusion protocol and efficient single cell dissociation yielding more than 500,000 podocytes per mouse allowing for global, unbiased downstream applications. Combining mRNA transcriptional profiling revealed programs of highly specific gene regulation tightly controlling cytoskeleton, cell differentiation, endosomal transport and peroxisome function in podocytes. Strikingly, the analyses further predict that these podocyte-specific gene regulatory networks are accompanied by alternative splicing of respective genes. In summary, the presented M-bM-^@M-^XomicsM-bM-^@M-^Y approach will facilitate the discovery and integration of novel gene, protein and organelle regulatory networks that deepen our systematic understanding of podocyte biology. To compare gene expression of glomerulus podocytes versus non-podocytes 5 replicates of 4 pooled mice were used. Data were normalized by robust multi-chip analysis. Exon expression values were summarised to the core meta probesets, as defined by Affymetrix, using the oligo library from R.

2012-11-30 | E-GEOD-39441 | biostudies-arrayexpress

Adrenal medulla (AM) from controls and SDHD-ESR mice

Project description:Several mechanisms have been proposed to account for Sdh-mutation-induced tumorigenesis, the most accepted of which is based on the constitutive expression of the hypoxia-inducible factor 1alpha (Hif1alpha) at normal oxygen tension, a theory referred to as pseudo-hypoxic drive. Other molecular processes, such as oxidative stress, apoptosis or chromatin remodeling have been also proposed to play a causative role. Nevertheless, the actual contribution of each of these mechanisms has not been definitively established. Moreover, the biological factors that determine the tissue-specificity of these tumors have not been identified. In this work, we made use of the inducible SDHD-ESR mouse, a conditional mutant in the SdhD gene, which encodes the small subunit of MCII, and that acts as a tumor suppressor gene in humans. We performed microarray analysis of adrenal medulla (AM) in order to identify other early gene expression changes elicited by SdhD deletion. 8 samples from heterozygous (+/-) and 8 samples from null mutants (SDHD-ESR), paired by two and hybrydized against a pool of 8 samples from homozygous wt (+/+) animals.

2013-11-15 | E-GEOD-52195 | 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