Transcriptional profiling of H9 human embronic stem cells (hESC) and hESC derived retinal pigment epithelium (RPE)
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ABSTRACT:
PROVIDER: PRJNA524714 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8645873.fastq.gz | Fastqsanger.gz | |||
| SRR8645874.fastq.gz | Fastqsanger.gz | |||
| SRR8645875.fastq.gz | Fastqsanger.gz | |||
| SRR8645876.fastq.gz | Fastqsanger.gz | |||
| SRR8645877.fastq.gz | Fastqsanger.gz |
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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
Project description:RPE was derived from hESC based on the protocol described in Zhu et al. PlosOne. 2013.
2020-02-28 | GSE127352 | GEO
Project description:We differentiated the human embryonic stem cell line H9 into retinal pigment epithelium (RPE) cells, to assess their transcriptomic profiles over time in culture. In-depth molecular analysis was performed by single cell RNA-Sequencing to access the molecular signature of RPE cells grown and harvested at two time points in culture (30 days and 369 days post passaging). We performed high-resolution comparisons at subpopulation and single-cell levels, to assess gene expression pathway signatures in RPE cells and upon aging in vitro. The hESC line H9 was grown to 70-80% confluence, transitioned to E6 medium for 2 days, with supplementation of N2 from day 2 until day 33. On day 33, medium was switched to RPEM (alpha-MEM, N1 supplement, 5% FBS, NEAA, Pen Strep Glutamine, taurine-hydrocortisone-triiodo-thyronin (THT)) for an additional 32 days. Cells were enzymatically passaged using 0.25% Trypsin EDTA and plated at 75,000 cells/cm2 on Matrigel growth factor reduced pre-coated plates (P1). Cells were subsequently harvested at day 30 (sample \\"YOUNG\\") and day 369 (sample \\"AGED\\"). Both samples were sorted for live cells using PI on a BD FACS Aria. Cells were centrifuged at 300g for 5 min and resuspended in PBS containing 0.04% BSA to a concentration of ~800-1000 cells/ µl. Approximately 17,400 cells were loaded onto a 10X chip single Cell 3′ Chips along with the reverse transcription master mix as per the manufacturer's protocol for the Chromium Single Cell 3′ v2 Library for a target recovery of 10,000 cells. Samples were then processed for sc Seq.
2020-08-26 | E-MTAB-8511 | biostudies-arrayexpress
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.
2013-03-20 | GSE36695 | GEO
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
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
Project description:Safety is the principle consideration with any clinical program, for which hESC and their derived products hold specific challenges. Differentiated cell products derived from hESC must be free from pluripotent cells as these could potentially form teratomas. One relevant clinical program is transplantation of retinal pigment epithelial cells (RPE) derived from hESC. This has potential for halting visual decline in conditions where the RPE layer is damaged such as age-related macular degeneration (AMD). In this study we show that whole genome gene expression analysis of SHEF1.3 starting material and the P0 pigmented RPE foci shows that the two cell types are distinct.
2016-07-03 | E-MTAB-4154 | biostudies-arrayexpress
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
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.
2014-11-03 | GSE50738 | GEO
Project description:The retinal pigment epithelium (RPE) provides vital support to photoreceptor cells and its dysfunction is associated with the onset and progression of age-related macular degeneration (AMD). Surgical provision of RPE cells may ameliorate AMD and thus it would be valuable to develop sources of patient-matched RPE cells for this application of regenerative medicine. We describe here the generation of functional RPE-like cells from fibroblasts that represent an important step toward that goal. We identified candidate master transcriptional regulators of RPEs using a novel computational method and then used these regulators to guide exploration of the transcriptional regulatory circuitry of RPE cells and to reprogram human fibroblasts into RPE-like cells. The RPE-like cells share key features with RPEs derived from healthy individuals, including morphology, gene expression and function, and thus represent a step toward the goal of generating patient-matched RPE cells for treatment of macular degeneration. Expression analysis was performed on induced retinal pigment epithelium-like cells.
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