RNAseq analysis of retinal microglia during early diabetes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA579063 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10333923.fastq.gz | Fastqsanger.gz | |||
| SRR10333924.fastq.gz | Fastqsanger.gz | |||
| SRR10333925.fastq.gz | Fastqsanger.gz | |||
| SRR10333926.fastq.gz | Fastqsanger.gz | |||
| SRR10333927.fastq.gz | Fastqsanger.gz |
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Project description:In order to evaluate the gene expression profile of retinal microglia cells in different age, we purified CD11b-positive microglia from the retinas of wild type C57BL/6 mice at 3, 12, 18, and 24 months age using cell sorting method with flow cytometry. Age-related genes from isolated retinal microglia were performed using 16 Affymetrix GeneChips of Mouse Exon 1.0ST Arrays. Gene expression level between consecutive age groups (i.e. between 3 and 12 months, 12 and 18 months, and 18 and 24 months) was examined to identify microglia relevant aging genes that demonstrated significant changes. We identified a total 719 genes that showed increasing or decreasing more than 1.5-fold change (p<0.05, one-way ANOVA) for at least one of the three inter age-group comparisons. These identified genes were subjected to a hierarchical cluster analysis to visualize trends in differential expression across individual biological repeats in the 4 age groups. The microglia cells were isolated from wild type C57BL/6 mice with microglia cell specific marker CD11b conjugated with FITC using flowcytometry sorting. The aging time point was designed as 4 groups: 3 moth, 12 month, 18 month and 24 month; each group includes 4 repeats. The total RNA was extracted from isolated retinal microglia cells and reverse transcripted to cDNA after amplification and labeling. The gene expression profile was detected with Affymetrix GeneChip of Mouse Exon 1.0ST Arrays
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Project description:Rat Retinal Müller cells from diabetic rats (diabetes duration 6 months) compared to Rat Retinal Müller cells from healthy rats. Diabetes was induced by streptozotozine. Diabetic rats were treated with small doses of insulin to prevent catabolism. Keywords: ordered
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Project description:Microglia are the tissue-resident macrophages of the retina and brain, being critically involved in organ development, tissue homeostasis, and response to cellular damage. Until now, little is known about the transcriptional profile of human retinal microglia and how they differentiate from peripheral monocytes, as well as from brain microglia. Additionally, the degree to which mice are suitable models for human retinal microglia is still not clear. The present study applies fluorescence-activated cell sorting to isolate human retinal microglia from enucleated eyes and compares their transcriptional profile with that of whole retinal tissue, as well as classical, intermediate and non-classical monocytes. In addition, human retinal microglia are compared to murine retinal microglia, isolated from at least two-years old Cx3cr1GFP/+ mice, as well as human brain microglia obtained from the literature. Several overexpressed genes were identified in retinal microglia when compared to whole retinal tissue, as well as classical, intermediate, and non-classical monocytes, among them IL1B, C2, C3, TREM2, P2RY12 and SPP1. In relation to whole retina sequencing, several risk genes, such as APOE and TGBR1, as well as PLXDC2 and ARHGAP22 associated with age-related macular degeneration (AMD) and diabetic retinopathy (DRP), were preferentially expressed in retinal microglia, indicating their potential pathophysiological involvement. The top expressed genes exhibited a strong consistency between retinal and brain microglia, among them CD74, SPP1, ACTB, FTL and C3. There was a high degree of similarity between human and murine retinal microglia, although there were several species-specific genes, revealing for which genes mice are suitable models for human retinal microglia. This study provides detailed insights into the molecular profile of human retinal microglia and indicate a high similarity to brain microglia. It advances our under-standing about their role in human retinal disease, such as AMD and DRP. The similarities and differences between human and mice will facilitate the transferability of knowledge between both species.
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