Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of renal medulla and cortex during postnatal development

ABSTRACT: The aim of this study is to establish a comprehensive transcriptome atlas that enables identification of key molecular pathways and morphogenic events regulating postnatal renal medulla/papillary and cortex development. To achieve this, a microarray expression profiling was performed on postnatal day 0-90 renal medulla and cortex obtained from CD1 male mice. Renal medulla and cortex were regionally dissected from postnatal day 0-90 CD1 male mice, and total RNA extracted for microarray expression profiling. Each time point consists of RNA pooled from 4 biological replicates, and an Agilent Bioanalyser test was performed to assess RNA integrity prior to sample pooling. The microarray data was analysed with the use of lumi and limma packages (Bioconductor) in R.

ORGANISM(S): Mus musculus

SUBMITTER: Dr. Yu Phua

PROVIDER: E-GEOD-72128 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Microarray profiling of renal medulla / papilla and cortex during postnatal development

Project description:The aim of this study is to establish a comprehensive transcriptome atlas that enables identification of key molecular pathways and morphogenic events regulating postnatal renal medulla/papillary and cortex development. To achieve this, a microarray expression profiling was performed on postnatal day 0-90 renal medulla and cortex obtained from CD1 male mice.

2016-01-12 | GSE72128 | GEO

Renal cortex and medulla microRNA and mRNA expression differences between hypertensive and normotensive patients

Project description:This SuperSeries is composed of the following subset Series: GSE28283: Renal cortex microRNA expression differences between hypertensive and normotensive patients GSE28344: Renal medulla microRNA expression differences between hypertensive and normotensive patients GSE28345: Renal cortex expression differences between hypertensive and normotensive patients GSE28360: Renal medulla expression differences between hypertensive and normotensive patients Refer to individual Series

2011-10-14 | E-GEOD-28260 | biostudies-arrayexpress

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.

2017-04-27 | GSE95611 | GEO

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

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

Renal medulla expression differences between hypertensive and normotensive patients

Project description:Identification of renal medulla genes whose expression differs between male individuals with high blood pressure and normal blood pressure using Affymetrix GeneChip Human Gene 1.0 ST Arrays. The Silesian Renal Tissue Bank, a collection of tissue which aimed to investigate candidate genes in human cardiovascular disease, was used to analyze the gene expression in hypertensive and normotensive patients. Approximately 1 cm3 of tissue from the healthy (unaffected by cancer) pole of the kidney was obtained immediately after surgery and transferred into containers with RNAlater (Ambion) and preserved at 70°C before mRNA extraction, which used a commercially available assay (RNeasy, Qiagen). Medulla and cortex were separated and individual RNA was obtained for each of them. No pooling was performed. After extraction of RNA, cRNA was prepared and arrays performed using Affymetrix GeneChip Human Gene 1.0 ST Arrays performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

2011-10-14 | E-GEOD-28360 | biostudies-arrayexpress

Multi-omic Analysis of Primary Human Kidney Tissues Identifies Medulla-Specific Gene Expression Patterns

Project description:The renal medulla is a specialized region of the kidney with important homeostatic functions. It has also been implicated in genetic and developmental disorders and ischemic and drug-induced injuries. Despite its role in kidney function and disease, the medulla’s baseline gene expression and epigenomic signatures have not been well described in the adult human kidney. Here we generate and analyze gene expression (RNA-seq), chromatin accessibility (ATAC-seq), chromatin conformation (Hi-C) and digital spatial profiling data from adult human kidney cortex and medulla. Using data from our carefully annotated specimens, we assign samples in the larger public GTEx database to cortex and medulla, thereby identifying several misassignments and extracting meaningful medullary gene expression signatures. Using integrated analysis of gene expression, chromatin accessibility and conformation profiles, we reveal insights into medulla development and function. Our datasets will also provide a valuable resource for researchers in the GWAS community for functional annotation of genetic variants.

2023-11-15 | GSE235841 | GEO

Renal medulla microRNA expression differences between hypertensive and normotensive patients

Project description:Identification of renal medulla microRNAs whose expression differs between male individuals with high blood pressure and normal blood pressure using Agilent Human miRNA Microarrays (V3, release 12.0). The Silesian Renal Tissue Bank, a collection of tissues which aimed to investigate candidate genes in human cardiovascular disease, was used to analyze the miRNA expression in hypertensive and normotensive patients. Approximately 1 cm3 of tissue from the healthy (unaffected by cancer) pole of the kidney was obtained immediately after surgery and transferred into containers with RNAlater (Ambion) and preserved at 70°C before mRNA extraction, which used a commercially available assay (RNeasy, Qiagen). Medulla and cortex were separated and individual RNA was obtained for each of them. No pooling was performed. After extraction of RNA, cRNA was prepared and arrays performed using Agilent Human miRNA Microarrays (V3, release 12.0) performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

2011-10-14 | E-GEOD-28344 | biostudies-arrayexpress

Mus musculus

Project description:Microarray profiling of renal medulla / papilla and cortex during postnatal development

| PRJNA293120 | ENA

RNA-seq of human kidney cortex and medulla

Project description:We report gene expression (RNA-seq) from macro-dissected human kidney cortex and medulla from 3 individuals

2023-11-22 | GSE212907 | GEO

Effects of water restriction on gene expression in mouse renal medulla

Project description:In order to identify novel gene targets of vasopressin regulation in the renal medulla, we performed a cDNA microarray study on the inner medullary tissue of mice following a 48 hour water restriction protocol. Three renal medulla of 3 water restricted (WR) mice and three control mice (C) were hybridized against each other such that each WR sample was hybridized against each C sample.

2010-06-30 | E-GEOD-3498 | 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