Revealing the angiopathy of lacrimal gland lesion in type 2 diabetes
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ABSTRACT:
PROVIDER: PRJNA742767 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15010153_1.fastq.gz | Fastqsanger.gz | |||
| SRR15010153_2.fastq.gz | Fastqsanger.gz | |||
| SRR15010154_1.fastq.gz | Fastqsanger.gz | |||
| SRR15010154_2.fastq.gz | Fastqsanger.gz | |||
| SRR15010155_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goals of this study are to compare type 2 diabetes lacrimal gland transcriptome profiling (RNA-seq) with the counterparts. Methods: Lacrimal gland mRNA profiles of 24 weeks T2DM mice (C57 mice with high fat diet + STZ intraperitoneal injection) and counterparts were enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and the produced RNA was used for construction library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The prepared RNA-seq libraries were qualified using Agilent 2100 Bioanalyzer and quantified by qPCR absolute quantification method. The sequencing was then performed using Illumina NovaSeq 6000. After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered <=16 bp reads with cutadapt software. The trimmed reads were aligned to a reference genome with Hisat2 software. The transcript abundance for each sample was estimated with StringTie (v1.2.3), and the FPKM values for gene level were calculated with R package Ballgown (v2.6.0). The differentially expressed genes (DEGs) analysis was also performed with Ballgown. Fold change (cutoff 1.5), p-value (cutoff 0.05) and FPKM (≥0.5 mean in one group) were used for filtering differentially expressed genes and transcripts. Conclusions: Our study represents the first detailed analysis of T2DM lacrimal gland transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results showed that the vascular related genes were altered in the T2DM.
2021-08-08 | GSE179231 | GEO
Project description:The transcriptional expression analysis of 17.5, 19.5 days embryonic lacrimal gland (LG), adult lacrimal gland, lacrimal gland stem cells (LGSCs) P2 cultured for 5, 7, 10, 14 days and LGSCs P6, P10, P20 cultured for 7 days, respectively.
2019-08-06 | GSE135398 | GEO
Project description:Background: The study of human lacrimal gland biology and development is limited. Lacrimal gland tissue is damaged or poorly functional in a number of disease states including dry eye disease. Development of cell based therapies for lacrimal gland diseases requires a better understanding of the gene expression and signaling pathways in lacrimal gland. Differential gene expression analysis between lacrimal gland and other embryologically similar tissues may be helpful in furthering our understanding of lacrimal gland development. Methods: We performed global gene expression analysis of human lacrimal gland tissue using Affymetrix ® gene expression arrays. Primary data from our laboratory was compared with datasets available in the NLM GEO database for other surface ectodermal tissues including salivary gland, skin, conjunctiva and corneal epithelium. Results: The analysis revealed statistically significant difference in the gene expression of lacrimal gland tissue compared to other ectodermal tissues. The lacrimal gland specific, cell surface secretory protein encoding genes and critical signaling pathways which distinguish lacrimal gland from other ectodermal tissues are described. Conclusions: Differential gene expression in human lacrimal gland compared with other ectodermal tissue types revealed interesting patterns which may serve as the basis for future studies in directed differentiation among other areas.
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Project description:To identify the transcriptomic signature of adenoid cystic carcinoma of the lacrimal gland (LGACC), we performed RNA sequencing on LGACC tumor samples and normal lacrimal gland samples.
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Project description:For a better understanding of diabetic angiopathy (DA), the potential biomarkers in lacrimal DA and its potential mechanism, we evaluated the morphological and hemodynamic alterations of lacrimal glands (LGs) in patients with type 2 diabetes and healthy counterparts by color Doppler flow imaging (CDFI). We further established a type 2 diabetic mice model and performed hematoxylin-eosin (HE) staining, immunofluorescence staining of CD31, RNA-sequencing analysis, and connectivity map (CMap) analysis. We found atrophy and ischemia in patients with type 2 diabetes and mice models. Furthermore, we identified 846 differentially expressed genes (DEGs) between type 2 diabetes mellitus (T2DM) and vehicle mice by RNA-seq. The gene ontology (GO) analysis indicated significant enrichment of immune system process, regulation of blood circulation, apoptotic, regulation of secretion, regulation of blood vessel diameter, and so on. The molecular complex detection (MCODE) showed 17 genes were involved in the most significant module, and 6/17 genes were involved in vascular disorders. CytoHubba revealed the top 10 hub genes of DEGs, and four hub genes (App, F5, Fgg, and Gas6) related to vascular regulation were identified repeatedly by MCODE and cytoHubba. GeneMANIA analysis demonstrated functions of the four hub genes above and their associated molecules were primarily related to the regulation of circulation and coagulation. CMap analysis found several small molecular compounds to reverse the altered DEGs, including disulfiram, bumetanide, genistein, and so on. Our outputs could empower the novel potential targets to treat lacrimal angiopathy, diabetes dry eye, and other diabetes-related diseases.
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Project description:Transcriptional Characterization of healthy lacrimal gland
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Project description:Tears are essential for the maintenance of the terrestrial animal ocular surface and the lacrimal gland is the source of the aqueous layer of the tear film. Despite the importance of the lacrimal gland in ocular health, molecular aspects of its development remain poorly understood. We have identified a noncoding RNA (miR-205) as an essential gene for lacrimal gland development. Knockout mice lacking miR-205 fail to develop lacrimal glands, establishing this noncoding RNA as a key regulator of lacrimal bud initiation. RNA-seq analysis uncovered several up-regulated miR-205 targets, including Inppl1, a negative regulator of Akt signaling. Data indicate that Akt signaling is required within lacrimal gland epithelia and is activated by Fgf10. Furthermore, combinatorial epistatic deletion of Fgf10 and miR-205 in mice exacerbates the lacrimal gland phenotype. We develop a molecular rheostat model where miR-205 modulates signaling pathways downstream of Fgf10 to regulate glandular development. These data show that a single microRNA is a key regulator for lacrimal gland initiation in mice and highlights the important role of microRNAs during organogenesis.
2017-04-01 | GSE95108 | GEO
Project description:RNA-Seq of embryonic, adult lacrimal gland and lacrimal gland stem cells
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Project description:The goal of this study is to find the transcriptional targets downstream of PI3K signaling during lacrimal gland development. We performed laser capture microdissection of the lacrimal gland epithelial tissue at embryonic day E14.5 from control embryos and mutant embryos containing lacrimal gland-specific deletion of PI3K subunits. After tissue harvest, RNA was extracted, conversion to cDNA and amplification was performed by Clontech SMART-seq v4 Ultra low input RNA kit,and cDNA library construction was performed using Nextera XT DNA library preparation kit by core facility at Columbia university prior to RNA sequencing. After preparation of cDNA library, each sample was sequenced using Illumina platform
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