Retinal pigment epithelial cells

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Transcriptomics (1222)
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Organisms

Homo sapiens (89)
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Repository

biostudies-arrayexpress (1254)
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geo (102)
pride (40)
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jPOST (1)
PAXDB (1)

Tissue

Retinal pigment epithelial cell (19)
Epithelial cell (16)
Cell culture (9)
Retinal pigment epithelium cell (8)
Retinal pigment epithelium cell line (5)
Retina (3)
Others (2)
Embryonic stem cell (2)
Retinal pigment epithelium (2)
Choroid (1)
Embryo (1)
Eye (1)
Primary cell (1)
Stem cell (1)

Disease

Normal (14)
Age related macular degeneration (8)
Disease free (5)
Breast cancer (4)
Prostate cancer (2)
Prostate carcinoma (2)
Retinal degeneration (2)
Perilobar nephrogenic rest (1)
Breast Carcinoma (1)
Ependymoma (1)
Tumor (1)
Not applicable (1)
Myeloid neoplasm (1)
Post-stasis (1)
Untreated prostate cancer (1)
Invasive lobular carcinoma (1)
Pre-diabetic, non-obese diabetic (NOD) (1)
Colon cancer (1)
Pre-diabetic (1)
Barrett's esophagus (1)
Chronic myelogenous leukemia (1)
S enteritidis (1)
Colorectal adenocarcinoma (1)
Carcinoma (1)
Lung cancer (1)
Adenocarcinoma (1)
Ovarian cancer (1)
Type 1 diabetes mellitus (DM-1) (1)
Glaucoma (1)
Melanomatosis (1)

Technology Type

Mass Spectrometry (40)
Shotgun proteomics (26)
Affinity purification coupled with mass spectrometry proteomics (6)
Data-independent acquisition (5)
Bottom-up proteomics (4)
Gel-based experiment (2)
SWATH MS (2)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
NMR spectroscopy (1)
Mass spectrometry (1)
Data-dependent acquisition (1)
HDMSE (1)

Instrument Platform

Illumina NovaSeq 6000 (42)
NextSeq 500 (36)
Illumina HiSeq 4000 (32)
Illumina HiSeq 2500 (26)
Illumina HiSeq 2000 (16)
Illumina MiSeq (6)
Illumina Genome Analyzer IIx (5)
NextSeq 2000 (5)
Affymetrix GeneChip Scanner 3000 7G (4)
Scanning hardware (4)
Element AVITI (3)
Microcentrifuge (3)
Axon Instruments GenePix 4000B scanner (3)
G2565BA DNA microarray scanner [Agilent] (3)
Illumina NovaSeq X (3)
NextSeq 550 (3)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
10X Genomics Chromium (2)
ScanArray Lite [PerkinElmer] (2)
ArrayWoRx Biochip Reader [Applied Precision] (2)
Axon- GenePix4000B (2)
Illumina Genome Analyzer II (2)
N/A (2)
DNBSEQ-G400 (2)
BGISEQ-500 (2)
Maxwell RSC instrument (1)
Bravo automated liquid handling robot station (Agilent) (1)
High-performance computing workstation (1)
Protocol computer workstation running R statistical software (1)
Thermal cycler (PCR); Covaris ME220 focused ultrasonicator; magnetic separation rack; Agilent TapeStation system (D5000 and D1000 ScreenTape assays); Qubit fluorometer or equivalent; microcentrifuge. (1)

Publication Date

2010 (174)
2013 (140)
2012 (140)
2014 (134)
2015 (118)
2011 (108)
2016 (89)
2008 (70)
2009 (55)
2021 (44)
2022 (43)
2026 (41)
2025 (38)
2023 (37)
2024 (30)
2007 (29)
2020 (27)
2017 (24)
2018 (19)
2006 (18)
2019 (16)
2004 (11)
2005 (6)
2002 (1)

UNIPROT ID/AC

89462.XP_006039585.1 (1)
89462.XP_006039600.1 (1)
89462.XP_006039626.1 (1)
89462.XP_006039630.1 (1)
89462.XP_006039638.1 (1)
89462.XP_006039640.1 (1)
89462.XP_006039668.1 (1)
89462.XP_006039674.1 (1)
89462.XP_006039692.1 (1)
89462.XP_006039695.1 (1)
89462.XP_006039696.1 (1)
89462.XP_006039697.1 (1)
89462.XP_006039706.1 (1)
89462.XP_006039712.1 (1)
89462.XP_006039721.1 (1)
89462.XP_006039726.1 (1)
89462.XP_006039730.1 (1)
89462.XP_006039752.1 (1)
89462.XP_006039756.1 (1)
89462.XP_006039757.1 (1)
89462.XP_006039762.1 (1)
89462.XP_006039763.1 (1)
89462.XP_006039783.1 (1)
89462.XP_006039794.1 (1)
89462.XP_006039815.1 (1)
89462.XP_006039816.1 (1)
89462.XP_006039820.1 (1)
89462.XP_006039846.1 (1)
89462.XP_006039847.1 (1)
89462.XP_006039864.1 (1)

ENSEMBL ID

ENSG00000170477 (2)
ENSG00000147251 (1)

CHEBI ID

CHEBI:46229 (2)
CHEBI:46905 (2)
CHEBI:17754 (2)
CHEBI:4167 (2)
CHEBI:35932 (2)
CHEBI:16704 (2)
CHEBI:16857 (2)
CHEBI:15891 (2)
CHEBI:18183 (2)
CHEBI:37024 (2)
CHEBI:6650 (2)
CHEBI:16958 (2)
CHEBI:18132 (2)
CHEBI:17287 (2)
CHEBI:17115 (2)
CHEBI:18050 (2)
CHEBI:32816 (2)
CHEBI:17553 (2)
CHEBI:17203 (2)
CHEBI:18019 (2)
CHEBI:16015 (2)
CHEBI:17196 (2)
CHEBI:16467 (2)
CHEBI:16977 (2)
CHEBI:15428 (2)
CHEBI:17053 (2)
CHEBI:16335 (2)
CHEBI:16919 (2)
CHEBI:16414 (2)
CHEBI:17191 (2)

Metabolite Name

Uridine (2)
Taurine (2)
Inosine (2)
Choline (2)
Creatine (2)
Adenosine (2)
Glycine (2)
Glycerol (2)
Beta-alanine (2)
Myo-inositol (2)
N-nicotinoylglycine (1)
Aldehydo-N-acetyl-D-glucosamine (1)
Lacto-N-difucohexaose I (1)
Streptomycin (1)
Lactulose (1)
Lactobionate (1)
UDP-alpha-D-glucose (1)
Lactodifucotetraose (1)
3-fucosyllactose (1)
N-lactoyl leucine (1)
Lacto-N-tetraose (1)
(R)-carnitine (1)
N-lactoyl valine (1)
N-lactoyl tyrosine (1)
N-lactoyl phenylalanine (1)
3-methyl-2-oxovaleric acid (1)
Cysteinylglycine disulfide* (1)
Maltol (1)
10-hydroxystearate (1)
1-(1-enyl-palmitoyl)-2-docosahexaenoyl-GPE (P-16:0/22:6)* (1)

First Public Date

2026 (22)
2024 (21)
2025 (17)
2022 (17)
2014 (14)
2023 (13)
2020 (12)
2021 (8)
2018 (8)
2017 (8)
2019 (4)
2015 (3)
2016 (2)
2013 (1)

Modelling Approach

Ordinary differential equation model (1)

Lab affiliation

Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital (2)
1.Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA 92697, USA 2.Department of Ophthalmic Research, Cleveland Clinic, Cleveland, OH 44195, USA 3.Department of Physiology & Biophysics, School of Medicine, University of California-Irvine, Irvine, CA 92697, USA (1)
1Department of Ophthalmology, Stem Cell Ocular Regenerative Medicine Center, Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. (1)
Adele Niessen Professor of Ophthalmology Vice Chair for Research FM Kirby Center for Molecular Ophthalmology Scheie Eye Institute University of Pennsylvania (1)
Baxter Laboratory for Stem Cell Biology Department of Microbiology & Immunology Stanford University School of Medicine 269 Campus Drive CCSR 3205b Stanford, CA 94305-5175 (1)
Baxter Laboratory for Stem Cell Biology Department of Microbiology & Immunology Stanford University School of Medicine (1)
Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry Department of Clinical Chemistry, University Medical Center Goettingen (1)
CNIO (1)
Centre For Eye Research Australia(CERA) (1)
Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, UK (1)
College of Medicine University of Arkansas for Medical Science (1)
Department of Medicine, section of Physiology and Biochemistry, University of Perugia (1)
Department of Pathology, Johns Hopkins Medical School, USA (1)
Department of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA (1)
Department of Radiation Oncology, University of Texas Health Science Center at San Antonio (1)
Division of Cancer Biology, Institute of Cancer Research, 237 Fulham road, London SW3 6JB, UK. (1)
Eye & Vison Health, Flinders University School of Medicine Flinders Medical Center Flinders University Australia (1)
Harvard Medical School (1)
Head of Laboratory of Neuro-Oncology, Neurology, Clinical & Cancer Proteomics (1)
Institute for Ophthalmic Research Eberhard-Karls University of Tuebingen Elfriede-Aulhorn-Str. 7 D-72076 Tuebingen. Germany. (1)
Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany (1)
Institute of Biochemistry Medical Faculty University of Cologne Germany (1)
Luxembourg Institute of Health 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg (1)
Max-Delbrueck Center, Berlin Institute of Health (BIH), Berlin, Germany (1)
Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (1)
Molecular and Cell Biology University of California, Berkeley (1)
Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge MA 02139, USA (1)
Professor, Virology Director of the Laboratory of Molecular Virology (1)
Research Unit Protein Science Helmholtz Center Munich Germany (1)
School of Optometry, the Hong Kong Polytechnic University, Hong Kong, China Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China Research Centre for SHARP Vision (RCSV), the Hong Kong Polytechnic University, Hong Kong, China Research Centre for Chinese Medicine (RCMI), the Hong Kong Polytechnic University, Hong Kong, China (1)

IsPrivate

False (1)

Classification

bacteria (2)

Study type

Transcription profiling by array (736)
RNA-seq of coding RNA (139)
ChIP-seq (85)
RNA-seq of coding RNA from single cells (45)
Methylation profiling by array (28)
Unknown experiment type (25)
ChIP-chip by tiling array (24)
Comparative genomic hybridization by array (22)
Other (18)
Methylation profiling by high throughput sequencing (18)
RNA-seq of non coding RNA (16)
Cell line - High-throughput sequencing (10)
Transcription profiling by RT-PCR (10)
MicroRNA profiling by array (9)
Transcription profiling by tiling array (8)
ChIP-chip by array (8)
DNA-seq (6)
RNA-seq of total RNA (6)
Proteomic profiling by array (5)
Genotyping by array (4)
ATAC-seq (3)
Cell line - Single-cell sequencing (2)
MNase-seq (2)
RNA-seq of non coding RNA from single cells (2)
Animal - High-throughput sequencing (2)
MicroRNA profiling by high throughput sequencing (2)
Spatial transcriptomics by high-throughput sequencing (2)
Bisulfite-seq (2)
PRO-seq (1)
GRO-seq (1)

Release Date

2010 (188)
2013 (169)
2015 (162)
2012 (156)
2014 (154)
2022 (142)
2016 (134)
2021 (130)
2020 (124)
2023 (114)
2011 (114)
2025 (110)
2024 (82)
2017 (77)
2008 (74)
2019 (73)
2009 (63)
2018 (61)
2007 (37)
2026 (31)
2006 (19)
2004 (13)
2005 (8)
2002 (3)
2003 (2)
2001 (1)
2000 (1)
1998 (1)
1996 (1)

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MicroRNA Expression in Human RPE Cells in Culture: Control vs Treated with IFN-? + TNF-? + IL-1?

Human retinal pigment epithelial (HRPE) cells in culture respond to inflammatory cytokines (IFN-? + TNF-? + IL-1? ) by increasing the expression of many cytokines and chemokines. The goal of this study was to delineate the role of miRNA in this process. We employed microarray analysis to study the e...

ORGANISM(S): Homo sapiens

2010-11-11 | E-GEOD-23979 | biostudies-arrayexpress

Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells

Retinal pigment epithelium (RPE) cells can be obtained through in vitro differentiation of both embryonic stem cell (ESC) and induced pluripotent stem cells (iPSC) for cell replacement therapy. We have previously identified 87 signature genes relevant to RPE cell differentiation and function through...

ORGANISM(S): Homo sapiens

2012-08-01 | E-GEOD-37686 | biostudies-arrayexpress

Integrated analysis of DNA methylation and RNA transcriptome during the differentiation of human pluripotent stem cells into retinal pigment epithelial cells

Using the paradigm of in vitro differentiation of hESCs/iPSCs into retinal pigment epithelial (RPE) cells, we have recently profiled mRNA and miRNA transcriptomes to define a set of RPE mRNA and miRNA signature genes implicated in directed RPE differentiation. In this study, in order to understand t...

ORGANISM(S): Homo sapiens

2014-05-28 | E-GEOD-43473 | biostudies-arrayexpress

Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration

To identify disease-specific transcriptional programs in retinal pigment epithelium (RPE) cells, fibroblasts from 43 patients with geographic atrophy (GA) were reprogrammed into induced pluripotent stem cells (iPSCs) before being differentiated into RPE and compared to those from 36 healthy individu...

ORGANISM(S): Homo sapiens

2022-06-20 | E-MTAB-11642 | biostudies-arrayexpress

Transcription profiling of mouse T cell response to ocular pigment epithelial cells - role of thrombospondin 1

Ocular pigment epithelium (PE) cells promote the generation of T regulators (PE-induced Treg cells). Moreover, T cells exposed to PE acquire the capacity to suppress the activation of bystander T cells via TGFbeta. Membrane-bound TGFbeta on iris PE cells interacts with TGFbeta receptors on T cells, ...

ORGANISM(S): Mus musculus

2008-06-13 | E-GEOD-5134 | biostudies-arrayexpress

Transcriptome Analysis and Molecular Signature of Human Retinal Pigment Epithelium

The retinal pigment epithelium (RPE) is a polarized cell layer that is critical for photoreceptor function and survival. Itâ€™s unique relationship to the photoreceptors and its specific physiology makes the RPE a critical determinant of human vision. Therefore we performed global expression profil...

ORGANISM(S): Homo sapiens

2010-04-28 | E-GEOD-18811 | biostudies-arrayexpress

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

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 we...

ORGANISM(S): Homo sapiens

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

Global gene expression analysis of human iPSC-derived Retinal Pigmented Epithelial (RPE) cells from LCA patients and unaffected persons

Our purpose was to investigate genes and molecular mechanisms involved in patients with Leber congenital amaurosis (LCA). Fibroblasts from two unrelated clinically-identified patients (Coriell) were reprogrammed to pluripotency by retroviral transduction. These human induced Pluripotent Stem Cells (...

ORGANISM(S): Homo sapiens

2015-01-21 | E-GEOD-43926 | biostudies-arrayexpress

Transcriptomic analysis of human retinal detachment (RD) reveals both inflammation and photoreceptor death

We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment. Data analysis reveals major involvement of the immune response in the disease and interindividual variation was monitored to unravel a second crucial aspect of the p...

ORGANISM(S): Homo sapiens

2012-03-06 | E-GEOD-28133 | biostudies-arrayexpress

Proteomic analysis of S-acylated proteins in human retinal pigment epithelial cells reveals the role of palmitoylation of Niemann–Pick type C1 protein in cholesterol transportation

Palmitoylation is a dynamic process which regulates the activity of the modified proteins. Retinal pigment epithelial (RPE) cells play pivotal roles in visual cycle and maintaining healthy photoreceptor cells. Dysfunctional RPE cells are often associated with degenerative retinal diseases. The aim o...

ORGANISM(S): Homo sapiens (Human)

2023-03-10 | PXD034896 | Pride

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