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

Transcriptome analysis identifies oxidative stress injury biomarkers for Diabetic Nephropathy

ABSTRACT: The early diagnosis of diabetic nephropathy (DN) is essential to improve the prognosis and manage patients affected by this disease. Standard biomarkers, including albuminuria and glomerular filtration rate, are limited to give a precise result. New molecular biomarkers are needed to identify better and predict DN disease evolution. Characteristic DN biomarkers can be identified using transcriptomic analysis. Blood samples were used to isolate RNA for microarray expression using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays, we evaluated the transcriptomic profile of controls , prediabetes, type-2 diabetes mellitus, and DN.

ORGANISM(S): Homo sapiens

SUBMITTER: Juan José Oropeza Valdez

PROVIDER: E-MTAB-12135 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Viral Profiles in Sjogren's Syndrome

Project description:A study was designed to further define the viral landscape within Sjogren's Syndrome (pSS) affected salivary gland tissue to identify potential viral-mediated triggers in the pathogenesis of this autoimmune disease. Viral Probes for Vertebrate Infecting Viral Families

2017-05-01 | E-GEOD-77599 | biostudies-arrayexpress

Expression analysis of Pea3, Erm and Er81 overexpression in mHypoA-2/12 cell line

Project description:Investigation of whole genome gene expression level changes in mHypoA-2/12 cells transfected Pea3-pCDNA3, Erm-pCDNA3, and Er81-pCDNA3 cells compared to pCDNA3 transfected cells as a control.

2020-10-28 | E-MTAB-8475 | biostudies-arrayexpress

Expression analysis of Pea3, Erm and Er81 overexpression in SH-SY5Y cell line

Project description:Investigation of whole genome gene expression level changes in SH-SY5Y cells transfected pCDNA3-Pea3, pCDNA3-Erm, and pCDNA3-Er81 cells compared to pCDNA3 transfected cells as a control.

2020-10-28 | E-MTAB-8473 | biostudies-arrayexpress

microRNA genetic variation, from population analysis to functional implications of allele variants associated with cancer

Project description:Total RNA samples from three independent transfection experiments of vectors containing two different allelic variants of 4 miRNAs (hsa-mir-146a, hsa-mir-196a2, hsa-mir-499a, hsa-mir-499b) and an empty vector. The selected variants are cancer associated SNPs located in cancer related miRNAs. The aim of this study is to identify functional explanations for those associations. HeLa cells were used for microarray expression experiments in Agilent SurePrint G3 Human Gene Expression microarrays (8x60k), which target over 60,000 well-annotated RefSeq transcripts starting from 300ng of total RNA. Data were analyzed using the Array File Maker (AFM) 4.0 software package (Array File Maker, Stanford, California).

2016-02-23 | E-MTAB-3990 | biostudies-arrayexpress

DNA-methylation of LTP-associated genes.

Project description:Long-term potentiation (LTP) of synaptic transmission is recognized as a cellular mechanism for learning and memory storage. Although de novo gene transcription is known to be required in the formation of stable LTP, the molecular mechanisms underlying synaptic plasticity remain elusive.This study investigates the DNA-methylation levels of promoters and CpG-islands of LTP-associated genes identified from Maag et al. 2015 (DOI: 10.3389/fnins.2015.00351) (See E-MTAB-3375).

2017-03-16 | E-MTAB-4919 | biostudies-arrayexpress

microRNA expression of K562, Me45 and HCT116, with or without p53 knock-out, treated with ionizing radiation.

Project description:MicroRNA expression was assessed in human cancer cells (K562, Me45, HCT116 wt and HCT116 p53-/-) treated with 4Gy of ionizing radiation. RNA was extracted from the cells 12 hours after irradiation and after 1h from non-treated controls.

2016-12-01 | E-MTAB-5197 | biostudies-arrayexpress

Identification of netwoks mirna-mrna interactions during osteoblast differentiation of human dental pulp stem cells

Project description:To evaluate the miRNA and mRNA expression profiles (miRNOME and transcriptome) we reconstructed networks identifying miRNAs and mRNA during in vitro osteogenic differentiation of human dental pulp stem cells (DPSC). The DPSCs were cultured in the DMEM + beta-glycerol phosphate, ascorbic acid and dexamethasone for 2 to 21 days. The microRNA or mRNA expression profiling during the differentiation process was analyzed through hybridizations with Agilent miRNA-microarray (8x15K format) or whole-human genome Agilent microarray (4x44K format).

2014-11-13 | E-MTAB-3010 | biostudies-arrayexpress

The effect of the autoimmune regulator (Aire) gene on the transcriptional expression profile of 3.10 mTEC cell line.

Project description:Medullary thymic epithelial cells (mTECs) contribute to self-tolerance through the ectopic expression of peripheral tissue antigens (PTAs) in the thymus. PTA expression in mTECs is largely dependent on the autoimmune regulator (Aire) gene. Here we used a Mus musculus mTEC cell line (3.10 mTEC line, which constitutively express Aire in culture) to knockdown Aire gene by means of siRNA transfection. Aire knockdown was confirmed by means of qRT-PCR and RNA-FISH (for Aire mRNA levels), immunofluorescence and western blot (for AIRE protein levels).The Agilent oligo microarrays were used to determine the large scale transcriptional expression profiles of control or Aire-knockdown 3.10 mTECs.

2015-12-31 | E-MTAB-3879 | biostudies-arrayexpress

The effect of Dicer knockdown on the transcriptional expression profile of 3.10 mTEC cell line.

Project description:Dicer, also known as endoribonuclease Dicer or helicase with RNase motif, cleaves double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into short mature double-stranded RNA fragments called small interfering RNA and microRNA, respectively. Medullary thymic epithelial cells (mTECs) express close to 90% of the protein-coding genome, besides they play an important role to self-tolerance through the ectopic expression of peripheral tissue antigens (PTAs) in the thymus. MicroRNAs are potent post-transcriptional regulators in developmental switches, lineage commitment and gene expression regulation, but their role in representation of the immunological self in mature mTECs is not fully understood. So we used a Mus musculus mTEC cell line (mTEC 3.10) to knockdown Dicer transcript by means of siRNA transfection and then observe the effect of Dicer knockdown in the transcriptional profile of messenger RNAs (mRNAs) by means of oligo microarray hybridization. The Agilent oligo microarrays were used to determine the large scale mRNA transcriptional profiles of control or Dicer-knockdown 3.10 mTECs.

2016-06-27 | E-MTAB-4628 | biostudies-arrayexpress

Identification of differentially expressed genes in human alveolar bone cells cultured on different titanium surfaces.

Project description:To evaluate mRNA expression profile (transcriptome), we identified mRNAs of osteoblastic cells from human alveolar crest culture in contact with different titanium surfaces: control (polished), nanotextured (polished titanium discs, etching at 25oC with 50% H2SO4conc and 50% H2O2aq) , nano+submicrotextured (polished titanium discs, etching at 50oC with 50% H2SO4conc and 50% H2O2aq) and rough microtexture (polished titanium discs, etching at 50oC with 100% H2O2aq). The osteoblastic cells were cultured in the alpha-minimum essential medium, supplemented with fetal bovine serum, gentamicin, fungizone, dexamethasone, ascorbic acid and β-glycerophosphate. The mRNA expression profiling was analyzed through hybridizations with whole-human genome Agilent microarray (4x44K format).

2014-11-14 | E-MTAB-3091 | 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