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RNA-seq of primary human fetal RPE cells (hfRPE) treated with IL1α with and without Zn supplementation against untreated controls

ABSTRACT: RNA-seq of primary human fetal RPE cells (hfRPE) treated with IL1α with and without Zn supplementation against untreated controls

PROVIDER: PRJEB53935 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR9883570_1.fastq.gz	Fastqsanger.gz
	ERR9883570_2.fastq.gz	Fastqsanger.gz
	ERR9883571_1.fastq.gz	Fastqsanger.gz
	ERR9883571_2.fastq.gz	Fastqsanger.gz
	ERR9883572_1.fastq.gz	Fastqsanger.gz

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RNA-seq of primary human fetal RPE cells (hfRPE) treated with IL1α with and without Zn supplementation against untreated controls

Project description:A RPE cell model mimicking a matured RPE was subjected to an acute inflammatory stress with and without Zn supplementation and the effects of such exposure were evaluated by studying alterations at the transcriptome level. The experiment performed aim to improve the understanding of the metabolic processes involving Zn and their relevance in the physiology and pathophysiology of neurodegenerative diseases resembling AMD disease.

2022-07-08 | E-MTAB-11891 | biostudies-arrayexpress

Effects of zinc supplementation in the temporal transcriptomic profiling of human primary fetal RPE cell using single-cell RNA sequencing

Project description:This is the first publication that assessed the complex molecular changes that underpin acute zinc supplementation-induced changes at the single cell RNA sequencing level in a well-characterised age-related macular degeneration (AMD) cell model. The retinal pigment epithelial (RPE) cells were allowed to mature for up to 19 weeks, during which time they developed sub-RPE deposits, a hallmark of AMD. Comparing the scRNA-Seq data from cells after two-, nine- and 19 weeks in culture, we identified distinct clusters of cells. Pseudotemporal ordering of the combined gene lists from all time points identified genes implicated in the dynamics of RPE cell differentiation, with enrichment in biologically plausible pathways. Acute (1 week) zinc supplementation (125 µM added zinc) resulted in the differential expression of several genes, including specific transcriptional regulators.

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Project description:To assess the geome-wide similarities between primary fetal retinal pigmented epithelium (RPE) and stem-cell derived RPE, we performed whole genome microarray expression on primary RPE and both embryonic stem cell (ESC) derived RPE and induced pluripotent stem cell (iPSC) derived RPE. We found ES-derived RPE better resembles fetal RPE than iPS-derived RPE. Gene expression was measured in primary fetal RPE, ES-derived RPE, iPS-derived RPE. ES cells and BJ fibroblasts were used as controls.

2010-11-10 | E-GEOD-25143 | biostudies-arrayexpress

Characterization of Stem-cell derived Retinal Pigmented Epithelium (RPE)

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The transcriptomic signature of diteray zinc supplementation in sheep

Project description:In the present study, we studied the effect of dietray zinc (Zn) supplementation on the transcriptome profile of lactating ewes. The main objective was to evaluate the effect of Zn-supplementation on the overall transcriptome and the altered pathways and biological processes in lactating ewes. A previously custom-designed oligo microarray platform (GPL20576) was used to profile the transcriptome of 15 ewes at two time points [T0 (before supplementation) and T40 (after 40-days supplementation period; n = 30). The Isolated and purified total RNAs were individually hybridized to the custom (4x44k) DNA microarray. The comparison of control and treated animal transcriptomes revealed a large set of differentially expressed genes. Functional analysis showed several pathways and biological processes that have been altered following Zn-supplementation to the diet.

2017-10-22 | GSE74779 | GEO

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.

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

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