Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-transcriptome sequencing analysis of streptozocin-induced diabetic and non-diabetic control rats

ABSTRACT: Diabetes mellitus is a complex metabolic disorder. Long-term hyperglycemia may induce diabetic keratopathy, which is mainly characterized by decreased tear secretion, damaged innervation, weakened cell junctions, and impaired wound healing responses. To investigate the differential expressed genes in the regulation of diabetic keratopathy, we established streptozocin-induced diabetic and non-diabetic control male Brown Norway rats. Total RNA was extracted from the corneal epithelium rats, and were subjected to whole-transcriptome sequencing analysis. Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Hisat2to map reads to the genome from corneal epithelium of streptozocin-induced diabetic and non-diabetic control rats. The mapped reads of each sample were assembled using String Tie. Then, all transcriptomes from corneal epithelium Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 corneas from STZ-induced diabetic rats and 6 corneas from normal controls.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE227165 | GEO | 2024/04/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Comprehensive analysis of differentially expressed microRNAs involved in diabetic trigeminal ganglion

Project description:Diabetic keratopathy(DK) is a common ocular complication of diabetes that seriously threatens diabetic patients' vision. Here, by sequencing of microRNAs (miRNAs) from diabetic and normal TG tissues, we aimed to uncover potential miRNAs involved in the pathogenesis of diabetic corneal neuropathy.

2023-10-18 | GSE245193 | GEO

Differentially Expressed Wound Healing-Related microRNAs in the Human Diabetic Cornea

Project description:MicroRNAs are powerful gene expression regulators, but their corneal repertoire and potential changes in corneal diseases remain unknown. Our purpose was to identify miRNAs altered in the human diabetic cornea by microarray analysis, and to examine their effects on wound healing in cultured telomerase-immortalized human corneal epithelial cells (HCEC) in vitro. Using microarrays, 29 miRNAs were identified as differentially expressed in diabetic samples. Two miRNA candidates showing the highest fold increased in expression in the diabetic cornea were confirmed by Q-PCR and further characterized. HCEC transfection with h-miR-146a or h-miR-424 significantly retarded wound closure, but their respective antagomirs significantly enhanced wound healing vs. controls. Cells treated with h-miR-146a or h-miR-424 had decreased p-p38 and p-EGFR staining, but these increased over control levels close to the wound edge upon antagomir treatment. In conclusion, several miRNAs with increased expression in human diabetic central corneas were found. Two such miRNAs inhibited cultured corneal epithelial cell wound healing. Dysregulation of miRNA expression in human diabetic cornea may be an important mediator of abnormal wound healing. Total RNA was extracted from age-matched human autopsy normal (n=6) and diabetic (n=6) central corneas, Flash Tag end-labeled, and hybridized to Affymetrix® GeneChip® miRNA Arrays. Select miRNAs associated with diabetic cornea were validated by quantitative RT-PCR (Q-PCR) and by in situ hybridization (ISH) in independent samples.

2013-11-09 | E-GEOD-52233 | biostudies-arrayexpress

Transcriptional Network Analysis Reveals the Role of miR-223-5p During Diabetic Corneal Epithelial Regeneration [RNA-seq]

Project description:Diabetes mellitus (DM) is a complex metabolic disorder. Long-term hyperglycemia may induce diabetic keratopathy (DK), which is mainly characterized by delayed corneal epithelial regeneration. MicroRNAs (miRNAs) have been reported to play regulatory roles during tissue regeneration. However, the molecular mechanism by which miRNAs influence epithelial regeneration in DK is largely unknown. In this study, we performed miRNA and mRNA sequencing of regenerative corneal epithelium tissue from streptozotocin-induced type 1 diabetic (T1DM) and wild-type mice to screen for differentially expressed miRNAs and mRNAs. Based on regulatory network analysis, miR-223-5p was selected for subsequent experiments and Hpgds was then identified as a direct target gene. MiR-223-5p downregulation significantly promoted diabetic corneal epithelial wound healing and nerve regeneration. However, the beneficial effects of miR-223-5p inhibition were abolished by an Hpgds inhibitor. Furthermore, mechanistic studies demonstrated that miR-223-5p suppression ameliorated inflammation and enhanced cell proliferation signaling in DK. Taken together, our findings revealed that the regulatory role of miR-223-5p in diabetic corneal epithelial and nerve regeneration by mediating inflammatory processes and cell proliferation signaling. And silencing miR-223-5p may contribute to the development of potential therapeutic strategies for DK.

2021-08-23 | GSE180490 | GEO

Transcriptional Network Analysis Reveals the Role of miR-223-5p During Diabetic Corneal Epithelial Regeneration [miRNA-seq]

2021-08-23 | GSE180493 | GEO

scRNAseq of diabetic corneal epithelium

Project description:scRNAseq of diabetic corneal epithelium

| PRJNA756322 | ENA

scRNAseq of diabetic corneal epithelium

Project description:We performed single cell transcriptional profiling of mouse corneal epithelium in streptozotocin-induced diabetic mice.

2022-12-19 | GSE182477 | GEO

Differentially Expressed Wound Healing-Related microRNAs in the Human Diabetic Cornea

2013-11-09 | GSE52233 | GEO

Single cell transcriptomic profiling of corneal epithelium of diabetic non-human primates reveals that FOXO3 regulates ROS by reprogramming glucose metabolism

Project description:Hyperglycemia leads to functional decline of various corneal cells, which induces corneal diseases. However, cellular and molecular mechanisms underlying how hyperglycemia affects the corneal epithelium have not been determined. Here, by undertaking single-cell transcriptomics of corneal epithelial cells obtained from healthy and diabetic non-human primates, we identified cell type-specific transcriptional alterations and shared changes across cell types, such as upregulation of FOXO3. Targeted depletion of FOXO3 in human corneal epithelial cells regulated metabolic remodeling by inhibiting glycolysis and oxidative phosphorylation. Furthermore, FOXO3 can not only sense reactive oxygen species (ROS) in corneal epithelial cells and scavenge ROS, but also mediate the proliferation and migration of corneal epithelial cells, demonstrating FOXO3 as a guardian factor in maintaining primate corneal epithelial homeostasis. Our study provides novel insight into the role of FOXO3 in metabolic remodeling and maintenance of ROS homeostasis in corneal epithelium at single-cell level, laying a foundation for decoding the molecular mechanism of the diagnosis and treatment of diabetic eye disease.

2024-12-19 | GSE197745 | GEO

Genome-wide analysis of miRNAs suggests a differential microRNAs signature associated with Normal and Diabetic limbal human corneas

Project description:Small non-coding RNAs, in particular microRNAs (miRNAs), regulate fine-tuning of gene expression and can impact a wide range of biological processes. Using deep sequencing analysis, we investigated miRNA expression profiles in central and limbal regions of normal and diabetic human corneas. We identified differentially expressed miRNAs in limbus vs. central cornea in normal and diabetic (DM) corneas including both type I (T1DM/IDDM) and type II (T2DM/NIDDM). Some miRNAs such as miR-10b that was upregulated in limbus vs. central corneas and in diabetic vs. normal limbus also showed significant increase in T1DM vs. T2DM limbus

2023-03-14 | GSE97069 | GEO

The tissue-engineered human cornea as a model to study expression of matrix metalloproteinases during corneal wound healing

Project description:Corneal injuries remain a major cause of consultation in the ophthalmology clinics worldwide. Repair of corneal wounds is a complex mechanism that involves cell death, migration, proliferation, differentiation, and extracellular matrix (ECM) remodeling. In the present study, we used a tissue-engineered, two-layers (epithelium and stroma) human cornea as a biomaterial to study both the cellular and molecular mechanisms of wound healing. Gene profiling on microarrays revealed important alterations in the pattern of genes expressed by tissue-engineered corneas in response to wound healing. Expression of many MMPs-encoding genes was shown by microarray and qPCR analyses to increase in the migrating epithelium of wounded corneas. Many of these enzymes were converted into their enzymatically active form as wound closure proceeded. In addition, expression of MMPs by human corneal epithelial cells (HCECs) was affected both by the stromal fibroblasts and the collagen-enriched ECM they produce. Most of all, results from mass spectrometry analyses provided evidence that a fully stratified epithelium is required for proper synthesis and organization of the ECM on which the epithelial cells adhere. In conclusion, and because of the many characteristics it shares with the native cornea, this human two layers corneal substitute may prove particularly useful to decipher the mechanistic details of corneal wound healing. Primary cultures of human corneal epithelial cells cultivated on BSA (number of replicates: 7), Collagen type I (number of replicates: 2), Collagen type IV (number of replicates: 2), Fibronectin (number of replicates: 2), Tenascin C (number of replicates: 2) and Laminin (number of replicates: 2) matrix. Central, internal and external ring of wounded Tissue-engineered human cornea.

2015-11-25 | E-GEOD-75336 | 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