Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Glomerular Transcriptome from European Renal cDNA Bank subjects and living donors

ABSTRACT: Glomerular Transcriptome from European Renal cDNA Bank subjects and living donors. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47183 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples). RNA from the glomerular compartment of was extracted and processed for hybridization on Affymetrix microarrays, annotated using Human Entrez Gene ID custom CDF version 19. This dataset is part of the TransQST collection.

ORGANISM(S): Homo sapiens

SUBMITTER: Sean Eddy

PROVIDER: E-GEOD-104948 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Metabolic pathways and immunometabolism in rare kidney diseases.

Grayson Peter C PC Eddy Sean S Taroni Jaclyn N JN Lightfoot Yaíma L YL Mariani Laura L Parikh Hemang H Lindenmeyer Maja T MT Ju Wenjun W Greene Casey S CS Godfrey Brad B Cohen Clemens D CD Krischer Jeffrey J Kretzler Matthias M Merkel Peter A PA

Annals of the rheumatic diseases 20180503 8

<h4>Objectives</h4>To characterise renal tissue metabolic pathway gene expression in different forms of glomerulonephritis.<h4>Methods</h4>Patients with nephrotic syndrome (NS), antineutrophil cytoplasmic antibody-associated vasculitis (AAV), systemic lupus erythematosus (SLE) and healthy living donors (LD) were studied. Clinically indicated renal biopsies were obtained at time of diagnosis and microdissected into glomerular and tubulointerstitial compartments. Microarray-derived differential ge ...[more]

PMID: 29724730

Similar Datasets

Shared molecular targets in the glomerular transcriptome from patients with nephrotic syndrome and ANCA-associated vasculitis

Project description:Glomerular transcriptome from human kidney biopsies in Neptune and ERCB. A subset of samples profiled in this analysis were also profiled in Series GSE68127, and in GSE104066. Corresponding tubulointerstitial transcriptome data is submitted under GEO ID: GSE108113. RNA from the glomerular compartment was extracted and processed for hybridization on Affymetrix ST 2.1 microarrays, annotated using Human Entrez Gene ID custom CDF version 19. This dataset is part of the TransQST collection.

2018-05-17 | E-GEOD-108109 | biostudies-arrayexpress

Glomerular Transcriptome from European Renal cDNA Bank subjects and living donors

Project description:summary : Glomerular Transcriptome from European Renal cDNA Bank subjects and living donors. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47183 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples).

2018-01-24 | GSE104948 | GEO

Tubulointerstitial transcriptome from ERCB subjects with chronic kidney disease and living donor biopsies.

Project description:Tubulointerstitial transcriptome from ERCB subjects with chronic kidney disease and living donor biopsies. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47184 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples). RNA from the tubulointerstitial compartment of was extracted and processed for hybridization on Affymetrix microarrays, annotated using Human Entrez Gene ID custom CDF version 19. This dataset is part of the TransQST collection.

2018-01-24 | E-GEOD-104954 | biostudies-arrayexpress

Proteomic analysis of plasma and duodenal tissue in patients with celiac disease: identification of potential diagnostic noninvasive biomarkers

Project description:The pathogenesis of celiac disease (CeD) remains incompletely understood. Traditional diagnostic techniques for CeD include serological testing and endoscopic examination; however, they have limitations. Therefore, there is a need to identify novel noninvasive biomarkers for CeD diagnosis. We analyzed duodenal and plasma samples from CeD patients by four-dimensional data-dependent acquisition (4D-DIA) proteomics. Differentially expressed proteins (DEPs) were identified for functional analysis and to propose blood biomarkers associated with CeD diagnosis. In duodenal and plasma samples, respectively, 897 and 140 DEPs were identified. Combining weighted gene co-expression network analysis(WGCNA) with the DEPs, five key proteins were identified across three machine learning methods. FGL2 and TXNDC5 were significantly elevated in the CeD group, while CHGA expression showed an increasing trend, but without statistical significance. The receiver operating characteristic curve results indicated an area under the curve (AUC) of 0.7711 for FGL2 and 0.6978 for TXNDC5, with a combined AUC of 0.8944. Exploratory analysis using Mfuzz and three machine learning methods identified four plasma proteins potentially associated with CeD pathological grading (Marsh classification): FABP, CPOX, BHMT, and PPP2CB. We conclude that FGL2 and TXNDC5 deserve exploration as potential sensitive, noninvasive diagnostic biomarkers for CeD.

2024-11-15 | PXD057692 | Pride

Glomerular transcriptome from subjects in the NEPTUNE cohort

Project description:Glomerular Transcriptome from subjects in the NEPTUNE cohort. A number of samples profiled in this analysis were also profiled in Series GSE68127, and Series GSE108113. RNA from the glomerular compartment of was extracted and processed for hybridization on Affymetrix microarrays. Contributor: NEPTUNE Consortium. This dataset is part of the TransQST collection.

2018-05-17 | E-GEOD-104066 | biostudies-arrayexpress

Tobacco smoke exposure-related pathway gene expression signature in the bronchial airway epithelium

Project description:Using primary human bronchial epithelial cells collected at bronchoscopy, we have perturbed signaling pathways important in regulation of response to tobacco smoke exposure and cancer development: ATM, BCL2, GPX1, NOS2, IKBKB, and SIRT1 Using gene expression profiles generated for each pathway and four independent gene expression datasets, we show that SIRT1 activity is significantly up-regulated in cytologically normal airway epithelial cells from active smokers compared to non-smokers; and in contrast, this activity is strikingly down-regulated in non-small cell lung cancer. 52 samples were run on Affymetrix Human Exon 1.0 ST microarrays (n=7 for ATM, n=8 for GPX1, n=7 for SIRT1, n=7 for NOS2, n=7 for IKBKB, n=8 for BCL2, and n=8 for GFP). The CEL files were processed using RMA and the ENTREZ Gene CDF file. 13 samples were removed either because of a low Pearson correlation between samples (n=1 SIRT1 sample) or a strong batch effect (n=2 ATM, n=2 BCL2, n=2 GFP, n=2 GPX1, n=1 IKBKB, n=2 NOS2, n=1 SIRT1 samples) as determined by PCA.

2012-09-27 | E-GEOD-37058 | biostudies-arrayexpress

Targeted Pten deletion plus p53-R270H mutation in mouse mammary epithelium induces aggressive claudin-low and basal-like breast cancer

Project description:WAP-Cre:Ptenf/f:p53lox.stop.lox_R270H composite mice were generated by genetic crossing. In these mice, Pten is deleted and a R270H p53 mutation in the DNA binding domain is induced upon expression of Cre recombinase in pregnancy-identified alveolar progenitors. Tumors were characterized by histology, marker analysis, various bioinformatics methods, high-throughput (HTP) FDA-drug screen as well as orthotopic injection to quantify tumor initiating cells (TICs) and tail-vein injection to identify lung-metastasis. Expression data comparing 2 types of Pten-deficient tumors (spindle and poorly differentiated) with other modles of mouse mammary tumors 2 types of Pten deletion plus p53-R270H mutation tumors (spindle and poorly differentiated) was compared with MMTV-Neu, Spindle Pten-p53-deficient tumors, and wild-type mammary gland cells.

2015-12-15 | E-GEOD-75989 | biostudies-arrayexpress

Identification of the Saccharomyces cerevisiae ZMP binders

Project description:5′-phosphoribosyl-5-amino-4-imidazole carboxamide monophosphate (ZMP) is a metabolic intermediate of the de novo purine biosynthesis pathway. Its accumulation in several cell types from bacteria to human is associated with growth impairment. Identification of ZMP-binding proteins was performed to understand the molecular basis of ZMP toxicity. To assess the specificity of ZMP-binding proteins, an affinity chromatography approach was also applied to the closely related molecules AMP, SZMP (Succinyl-ZMP) and AICAR (5-amino-4-imidazole carboxamide ribonucleoside, also named Acadesine).

2018-11-21 | PXD007780 | Pride

Transcription profiling of liver, skeletal muscle and white adipose tissue from ApoE3L mice

Project description:Our aim was to investigate gene expression changes over time in liver of ApOE3*Leiden mice on a high-fat diet. Probesets were remapped and annotated into Entrez gene-ids using the custom MBNI CDF-file, version 9.0.1 - the GCRMA data generated

2010-07-28 | E-TABM-1039 | biostudies-arrayexpress

RNA-Seq of human AML cell line, HL-60 and its mitoxantrone resistant subline HL60/MX2

Project description:Alteration in metabolic repertoire is commonly associated with resistance phenotype. Although it’s a common phenotype, not much efforts have been undertaken to design effective strategies to target the metabolic drift in such cancerous cells and especially with drug resistant properties. In our study, we identified that drug resistant AML cell line HL-60/MX2 do not follow classical Warburg effect, instead these cells exhibit drastically low levels of aerobic glycolysis. Biochemical analysis confirms reduced glucose consumption and lactic acid production by resistant population with no differences in glutamine consumption. Raman spectroscopy revealed increased lipid and cytochrome content in resistant cells which were also visualized in the form of lipid droplets by Raman mapping, electron microscopy and lipid specific staining. Gene set enrichment analysis data from both the cell lines revealed significant enrichment of lipid metabolic pathways in HL-60/MX2 cells. Further drug resistant cells possess higher mitochondrial activity and increased OXPHOS suggested the role of fatty acid metabolism as energy source which was confirmed by increased rate of fatty acid oxidation. Pharmacological inhibition of fatty acid oxidation using Etomoxir affected the colony formation ability of resistant cells and inhibition of OXPHOS using Antimycin-A increased the sensitivity of resistant cells to chemotherapeutic drug, demonstrating requirement of fatty acid metabolism and increased dependency on OXPHOS by resistant leukemic cells for tumorigenicity.

2021-01-01 | E-MTAB-8981 | 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