Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-sequencing analysis of VEGFR2 knocking down in retinal pigment epithelial (RPE) cells upon glucose depletion.

ABSTRACT: RNA-sequencing analysis of VEGFR2 knocking down in retinal pigment epithelial (RPE) cells upon glucose depletion.

PROVIDER: PRJNA689320 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13345300_1.fastq.gz	Fastqsanger.gz
	SRR13345300_2.fastq.gz	Fastqsanger.gz
	SRR13345301_1.fastq.gz	Fastqsanger.gz
	SRR13345301_2.fastq.gz	Fastqsanger.gz
	SRR13345302_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

RNA-sequencing analysis of VEGFR2 knocking down in retinal pigment epithelial (RPE) cells upon glucose depletion.

Project description:RNA-sequencing analysis was utilized to investigate the impact of VEGFR2 knockdown via siRNA on transcriptome profiling in primary human RPE cells under the glucose depletion condition compared to the control siRNA.

2021-06-16 | GSE164167 | GEO

THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE]

Project description:Loss of the retinal pigment epithelium (RPE) due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self-repair is an attractive therapeutic strategy; however, mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues, including the RPE, but little is known about the mechanisms that drive RPE regeneration. Here, utilizing zebrafish, we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post-RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro-regenerative environment in mammals.

2021-05-17 | GSE155294 | GEO

Expression data from human induced pluripotent stem cells derived retinal pigment epithelium (hiPSC-RPE)

Project description:We generated hiPSCs from patients fibloblast with retinitis pigmentosa (RP) using retrovirus and Sendai virus vectors, which we differentiated into hiPSC derived retinal pigment epithelium using two different methods (SDIA and SFEB methods). We investigated whether these hiPSC-RPE colonies, which were differentiated from various cell lines and methods, showed similar gene expression patterns to those of native RPE. We classified hiPSC-RPE, hiPSCs, and fibroblasts from RP patients, hRPE (commercially available human fetal RPE, Lonza) , ARPE19 (a human RPE cell line), and other human tissues from 54,675 probe sets using microarray data.

2014-11-03 | E-GEOD-50738 | biostudies-arrayexpress

Comparison of stem-cell derived retinal pigment epithelia (RPE) with human fetal retina pigment epithelium

Project description:Retinal Pigment Epithelium (RPE) derived from two human embryonic stem cell lines, H1 and H9, were compared with human fetal RPE (hfRPE) using RNA-seq. Nominally, the transcriptome of H1-derived RPE showed greater overlap with hfRPE. For cells maintained in the medium used to differentiate RPE, 6.2% (H1-RPE) and 4.2% (H9-RPE) of the transcripts were expressed in amounts that were statistically different from hfRPE (false discovery rate: 5%). After adaptation to the serum-free medium, SFM-1, only 1.0 % (H1-RPE) and 1.9% (H9-RPE) were expressed in amounts that were statistically different. For RPE signature genes, statistical differences were observed for 1.0 % (H1-RPE) and 1.9% (H9-RPE) of the transcripts. For some barrier-function related mRNAs the statistical differences were greater than these small differences would predict. For adhesion proteins and plasma membrane transporters, the differences were as great as 6.9% and 4.3%, respectively. After adaptation to SFM-1, the statistical differences between H1- and H9-RPE were only 0.4% for all transcripts, 1.4% for signature genes, and 0.7% for membrane transporters. No statistical differences were observed for the transcripts related to tight junctions, adhesion junctions or ion channels. In summary, SFM-1 promoted the maturation of stem cell-derived RPE, and the statistical difference between two stem cell lines was minimal. RNA sequencing of hfRPE from three fetuses (reference sample) and three independent isolates of RPE derived from the H1, and three from the H9, human embryonic stem cell (hESC) lines. The cultures were maintained in a serum-free medium, SFM-1. Comparisons were also made to cultures maintained in the medium used to differentiate the cells, KSR.

2013-03-20 | E-GEOD-36695 | biostudies-arrayexpress

Characterization of hES derived Retinal Pigment Epithelial (RPE). RPE proliferation involves a non-classical Epithelial-Mesenchymal Transition (EMT).

Project description:Retinal Pigment Epithelial (RPE) cells are located behind the retina and are critical for photoreceptor survival. Loss of RPE is associated with several pathogenic conditions such as Age Related Macular Degeneration and Retinitis Pigmentosa. RPE derived from human embryonic stem cells (hESC) offer a potential source for producing these cells for therapy. Here we report the molecular and cellular characterization of RPE differentiated from hESC. hESC derived RPE are capable of proliferation and lose their epithelial characteristics before becoming confluent and re-differentiating back into their typical pigmented, cobblestoned appearance. During the proliferative phase, they adopt a mesenchymal morphology and express mesenchymal markers. Our results demonstrate that this apparent Epithelial-Mesenchymal Transition is not regulated by the classical EMT transcription factors SNAIL and SLUG. Furthermore, it is possible to regulate RPE de-differentiation and re-differentiation by modulating the Wnt and BMP pathway respectively. These findings further our understanding of the genesis and expansion of RPE which is essential for their therapeutic use.

2012-10-24 | E-MTAB-854 | biostudies-arrayexpress

Comparison of stem-cell derived retinal pigment epithelia (RPE) with human fetal retina pigment epithelium

2013-03-20 | GSE36695 | GEO

Gene expression of cultured human choroidal stromal fibroblasts and retinal pigment epithelial (RPE) cells

Project description:Retinal pigment epithelial (RPE) cells and choroidal stromal fibroblast (CSF) were isolated from healthy human donor eyes. Cells were cultured and RNA extracted.

2018-11-25 | GSE122885 | GEO

Expression data from human induced pluripotent stem cells derived retinal pigment epithelium (hiPSC-RPE)

2014-11-03 | GSE50738 | GEO

RNA-seq of retinal pigment epithelium (RPE) derived from human induced pluripotent stem cells (iPSCs): healthy control and USH1B patient iPSCs

Project description:Compare transcriptomes of control and USH1B patient iPSC-derived retinal pigment epithelium (RPE) to elucidate disease mechanisms of Usher syndrome type IB (USH1B). USH1B patient fibroblasts were collected at Great Ormond Street Hospital (GOSH) and reprogrammed to iPSCs. Control and patient iPSCs differentiated in vitro to generate retinal pigment epithelium (RPE) and collected for RNA-seq at 24 week. Sequencing was performed at University College London (UCL) Genomics on a NovaSeq 6000 system. Data aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b.

2023-08-22 | E-MTAB-12165 | biostudies-arrayexpress

Pigment Epithelium Derived Factor (PEDF) secreted from iPSC derived-RPE facilitates apoptotic causes cell death, not the differentiation, of iPSCs

Project description:We show that Retinal pigment epithelium (RPE) secreted-factor, pigment epithelium derived factor (PEDF) secreted/derived from primary or iPSC-derived retinal pigment epithelium (RPE)RPE, dramatically inhibitsed the cell growth of iPSCs. PEDF was detected abundantly in culture supernatant media of primary and iPSC-derived RPE. We examined the gene expression in primary RPE and iPS-derived RPE. Two samples: RPE derived from 253G1 iPSC, Primary RPE.

2013-01-03 | E-GEOD-43257 | 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