Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic Analysis of Endothelial Cells from Fibrovascular Membranes in Proliferative Diabetic Retinopathy

ABSTRACT: Purpose: Identification of RUNX1 via next-generation sequencing (NGS) of fibrovascular membranes in patients with proliferative diabetic retinopathy. Methods: Transcriptomic analysis with Illumina HiSeq2000 of fibrovascular membrane and control retina CD31+ samples. The sequence reads were analyzed with ANOVA (ANOVA) and targets with significance (fold change > +/-1.5 and p-value < 0.05) were selected for with Cufflinks, DeSeq2, Partek E/M, and EdgeR. qRT–PCR validation was performed using SYBR Green assays along with Western blots, siRNA, and MUSE proliferation assays. Results: Using an optimized data analysis workflow, we mapped sequence reads per sample to the human genome (hg19) and identified genes that were statistically significant in all four statistical packages. P-values ranged from 8.78E-10 to 0.05. Using this gene list for ontology, highly significant annotation clusters included inflammatory, vascular development, and cell adhesion pathways. Conclusions: Our study represents the first detailed transcriptomic analysis of CD31+ cells from fibrovascular membrane and CD31+ cells from control retinas with biologic replicates, generated by RNA-seq technology. The preferential selection of inflammatory and angiogenic pathways using this gene list is highly consistent with DR pathogenesis, which involves leaky and aberrant vessel growth.

ORGANISM(S): Homo sapiens

PROVIDER: GSE94019 | GEO | 2017/04/04

SECONDARY ACCESSION(S): PRJNA363068

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptomes of CD31+CD34+HEPs with different expression of CD105 derived from human early hematopoietic differentiation by RNA Sequencing

Project description:Purpose: The goals of this study are to dessect the molecular signature of CD31+CD34+HEPs with different expression of CD105 ,and to explore the regulators such as signaling and transcription factors of CD105+ cells' generation. Methods: mRNA profiles of HEPs samples collected at day4 of hematopoietic differentiation were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions: The CD31+CD34+CD105-HEPs possess hematopoietic potential whereas the CD31+CD34+CD105+HEPs possess endothelial potential. In addition, the generation of CD105+cells were regulated by TGFbeta signaling and ETS1.

2018-12-15 | GSE123840 | GEO

Single cell transcriptomic analysis of proliferative diabetic retinopathy fibrovascular membranes reveals AEBP1 as fibrogenesis modulator.

Project description:The management of preretinal fibrovascular membranes, a devastating complication of advanced diabetic retinopathy (DR), remains challenging. We characterized the molecular profile of cell populations in these fibrovascular membranes to identify new therapeutic targets. Preretinal fibrovascular membranes were surgically removed from patients and submitted for single cell RNA (scRNA) sequencing. Differential gene expression was implemented to define the transcriptomic profile of these cells and revealed the presence of endothelial, inflammatory, and stromal cells. Endothelial cell re-clustering identified subclusters characterized by non-canonical trascriptomic profile, and active angiogenesis. Deeper investigation of the inflammatory cells showed a subcluster of macrophages expressing pro-angiogenic cytokines, presumably contributing to angiogenesis. The stromal cell cluster included a pericyte-myofibroblast transdifferentiating subcluster, indicating the involvement of pericytes in fibrogenesis. Differentially expressed gene analysis showed that Adipocyte Enhancer-binding Protein 1, AEBP1, was significantly upregulated in myofibroblast clusters, suggesting that this molecule may have a potential role in transformation. Cell culture experiments with human retinal pericytes (HRP) in high glucose condition confirmed the molecular transformation of pericytes towards myofibroblastic lineage. siAEBP1 transfection in HRP reduced the expression of profibrotic markers in high glucose. In conclusion, AEBP1 signaling modulates pericyte-myofibroblast transformation, suggesting that targeting AEBP1 could prevent scar tissue formation in advanced DR.

2023-11-02 | GSE245561 | GEO

Gene Expression Profile of Fibrovascular Membrane Associated with Proliferative Diabetic Retinopathy

2014-08-16 | GSE60436 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human ESCs early hematopoietic differentiation

Project description:Purpose:hESCs hematopoietic differentiation recapitulates embryonic hematopoiesis in vivo and occurs through three main stages: mesoderm commitment, hemogenic endothelium (HE) formation and hematopoietic specification. The goal of this study are to increase the understanding of hESCs hematopoietic differentiation process and its regulatory mechanism. Methods: hESC samples were collected through flow cytometry sorting.mRNA profiles of this samples were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions: Compared with other three populations, 57 cell surface markers were highly enriched in CD31+CD34+ endothelial cells.

2018-12-19 | GSE124062 | GEO

The genetics of wound healing in tympanic membranes in rats

Project description:The aim of this study was to identify the genes differentially expressed between timepoints in the week following tympanic membrane perforation in rats. Tissue from 240 individual rats was used in this study following random allocation into timepoint groups to be sacrificed over 7 days. An Agilent one color microarray technique was performed and the results were analyzed using Genespring GX9 software. A total of 3262 genes were identified as significant (p<0.05) and differentially expressed above a two-fold threshold between the timepoints. This study provides a complete genetic review of rat tympanic membrane wound healing over 7 days. The results can be used as a model for other wound healing in other mammals and in different parts of the body. The information on differential gene expression can be used in research towards developing chronic tympanic membrane perforations and also in research to treat acute and chronic tympanic membrane perforations. The microarray was performed on animals in a disease free environment and the genetic information can be compared to future research in disease states of the TM including Otitis media, cholesteatoma, chronic perforation and tympanosclerosis.

2009-08-19 | GSE17698 | GEO

The genetics of wound healing in tympanic membranes in rats

2010-08-18 | E-GEOD-17698 | biostudies-arrayexpress

miRNA profile in the vitreous of proliferative vitreoretinal disease patients

Project description:The microRNA profiles in the vitreous of proliferative vitreoretinal disease (PVD) such as proliferative diabetic retinopathy with fibrovascular membrane and macular hole (MH) patients were studied by RT-PCR.

2015-11-02 | GSE74559 | GEO

To determine the potential molecular mechanisms by which STAT5 signaling controls colonic crypt homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq).

Project description:Reads were aligned to the mm10 genome with annotations provided by Ensembl. Transcripts were filtered, requiring at least 3 reads in 50% of samples within at least one condition. To identify differentially-regulated transcripts, we performed ANOVA (FDR-corrected p<0.05) and required the fold change to exceed 1.5.

2019-04-02 | GSE112607 | GEO

Gene Expression Profile of Fibrovascular Membrane Associated with Proliferative Diabetic Retinopathy

Project description:Proliferative diabetic retinopathy (PDR) is a vision-threatening disorder characterized by the formation of cicatricial fibrovascular membranes leading to traction retinal detachment. Despite the recent advance in the treatment of PDR such as vitreoretinal surgery with use of anti-vascular endothelial growth factor (VEGF) drug as an adjunct, it still remains vision-threatening disease. In order to identify genes associated with the pathogenesis of PDR, we performed gene expression analyses in fibrovascular membrane in patients with PDR using DNA microarray technology. This study was approved by the Ethics Committee of the Kyushu University Hospital and Fukuoka University Chikushi Hospital, and the surgical specimens were handled in accordance with the ethical standards of the 1989 Declaration of Helsinki. All patients gave informed consent before inclusion in the study. Fibrovascular membranes (FVMs) were surgically dissected from the retinal surface with horizontal scissors of patients with PDR undergoing pars plana vitrectomy. These specimens were classified into active and inactive according to the clinical findings of neovascularization (NV) in the FVMs.Total RNA were extracted from the FVMs. RNA from human retina was obtained from Clontech (Palo Alto, CA).

2014-08-16 | E-GEOD-60436 | biostudies-arrayexpress

Mass spectrometry-based analysis of Muse cells from different origins

Project description:Multilineage-differentiating stress enduring (Muse) cells are nontumorigenic endogenous pluripotent-like stem cells easily collected from various adult or fetal tissues. The tissue regenerative effects of Muse cells have been demonstrated in many disease models, as they reach damaged sites after intravenous injection to exert pleiotropic effects. Previous reports indicate that several human tissues are readily accessible for Muse cell isolation, including adult tissues such as bone marrow (BM) and embryonic tissues such as Wharton’s Jelly (WJ) from umbilical cord. Wa analyzed the protein repertoires of WJ-Muse and BM-Muse using mass spectrometry-based proteomics.

2023-07-17 | PXD036883 | Pride

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