Photoreceptor - OmicsDI

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Organisms

Mus musculus (247)
Homo sapiens (119)
Drosophila melanogaster (66)
Danio rerio (41)
Arabidopsis thaliana (21)
Rattus norvegicus (11)
Gallus gallus (7)
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unidentified (3)
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synthetic construct (2)
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Repository

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pride (57)
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Tissue

Retina (23)
Cell culture (7)
Brain (4)
Retinal rod (4)
Photoreceptor cell (3)
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Eye photoreceptor cell (2)
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Photoreceptor layer of retina (2)
Cell suspension culture (1)
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Eye (1)
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RMC-1 cell (1)
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Disease

Not Available (4)
Disease free (4)
Retinal degeneration (3)
Retinal disease (2)
Parkinson's disease (2)
Breast cancer (2)
Retinitis pigmentosa (2)
Cerebral degeneration (1)
Huntington's disease (1)
Ocular albinism (1)
Retinal detachment (1)
Photoreceptor degeneration (1)
Hereditary pheochromocytoma (1)
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Normal (1)
Age related macular degeneration 1 (1)
Alzheimer's disease (1)
Bardet-Biedl syndrome 1 (1)
Blindness (1)
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Night blindness (1)
Retinal degeneration (1)

Technology Type

Mass Spectrometry (57)
Shotgun proteomics (27)
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Data-dependent acquisition (9)
Affinity purification coupled with mass spectrometry proteomics (8)
Mass spectrometry (6)
Chemical cross-linking coupled with mass spectrometry proteomics (6)
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Illumina HiSeq 2000 (3)
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HDMSE (2)
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AB SOLiD 4 System, Illumina HiSeq 2000 (1)
SRM/MRM (1)

Instrument Platform

Illumina NovaSeq 6000 (27)
NextSeq 500 (14)
Dell PowerEdge R750; CPU: 2 × Intel Xeon Gold 6346 (32 Cores / 64 Threads); RAM: 188 GB (5)
Illumina HiSeq 2500 (5)
Illumina HiSeq 2000 (5)
NucleoSpin RNA/Protein kit lysis buffer (350 µL per tube; Macherey‑Nagel). (4)
FastPrep‑24 homogenizer (MP Biomedicals) (3)
See manuscript (3)
NextSeq 2000 (3)
Nanostring GeoMx spatial profiler (2)
Axon GenePix4000B (2)
Illumina HiSeq (2)
Illumina Genome Analyzer IIx (2)
Axon- GenePix4000B (2)
Illumina Genome Analyzer II (2)
NextSeq 1000 (2)
Racham server on Uppmax, NAISS (2)
FACS Aria-III (2)
- (2)
NextSeq 550 (2)
Nanostring GeoMx® spatial profiler (1)
Real-time PCR Thermal Cycler (1)
Thermomixer (1)
FastPrep‑24 homogenizer (MP Biomedicals), operated at 5 m/s for 10 seconds. (1)
RapidPURE RNA Plant Kit (MP Biomedicals, Illkirch, France) (1)
FastPrep-24 homogeniser (1)
Element AVITI (1)
Non (1)
0.7 W LED light (1)
Ion Chef™ System and Ion S5™ System or Ion GeneStudio™ S5 Systems. (1)

Publication Date

2013 (154)
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2001 (1)
2004 (1)

UNIPROT ID/AC

P34057 (1)
O54828 (1)
Q9WVL4 (1)
P15409 (1)
O35599 (1)
Q8CFY0 (1)
P09174 (1)
Q3U6B2 (1)
P20443 (1)
P27600 (1)

CHEBI ID

CHEBI:28300 (3)
CHEBI:25017 (3)
CHEBI:15428 (3)
CHEBI:6650 (3)
CHEBI:18012 (3)
CHEBI:30915 (3)
CHEBI:17822 (2)
CHEBI:26271 (2)
CHEBI:25094 (2)
CHEBI:18237 (2)
CHEBI:16238 (2)
CHEBI:17239 (2)
CHEBI:22660 (2)
CHEBI:22653 (2)
CHEBI:184023 (2)
CHEBI:48928 (2)
CHEBI:18186 (2)
CHEBI:26986 (2)
CHEBI:16811 (2)
CHEBI:18257 (2)
CHEBI:17533 (2)
CHEBI:16708 (2)
CHEBI:24898 (2)
CHEBI:340824 (2)
CHEBI:37654 (2)
CHEBI:15741 (2)
CHEBI:16356 (1)
CHEBI:29108 (1)
CHEBI:15996 (1)
CHEBI:17552 (1)

Metabolite Name

Leucine (3)
Glycine (3)
Uridine (2)
Tryptophan (2)
Thymine (2)
Serine (2)
Proline (2)
Malate (2)
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Sucrose (2)
Succinic acid (2)
Naringenin chalcone (1)
Bisphenol A monosulfate (1)
3-hydroxytetradecanedioate (1)
Deoxythymidine diphosphate-l-rhamnose (1)
Succinyl CoA (1)
Prephenic acid (1)
Tetratriacontane (1)
N-tri(hydroxymethyl)methyltaurine (1)
L-ribonic acid (1)

First Public Date

2026 (103)
2025 (86)
2014 (80)
2022 (66)
2021 (63)
2024 (62)
2023 (44)
2019 (42)
2020 (39)
2017 (26)
2016 (23)
2018 (20)
2015 (19)
2013 (7)

Modelling Approach

Ordinary differential equation model (2)
Differential equation model (1)

Lab affiliation

Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada (3)
Boston Children's Hospital (2)
Light, Photosynthesis & Metabolism (LPM) & Exploring the Dynamics of Proteomes (EDyP) IRIG, CEA-Grenoble 17 rue des Martyrs, 38000 Grenoble, France (2)
Neuroproteomics Group Department of Molecular Neurobiology Max Planck Institute for Multidisciplinary Sciences Hermann-Rein-Str. 3 37075 Goettingen Germany (2)
Washington University in St. Louis School of Medicine (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)
1Brunason Center for Translational Vision Research, Department of Ophthalmology and Visual Sciences, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, 92697, USA; 2Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA; 3Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697, USA (1)
Aarhus University (1)
Associate Professor, University of Maryland College Park, MD 20742 (1)
Barbara M. Braunger, Institute of Neuroanatomy, University Clinic Hamburg-Eppendorf, Hamburg, Germany (1)
Bascom Palmer Eye Institute University of Miami (1)
Bioanalytical Mass Spectrometry Group,Max-Planck-Institute for Multidisciplinary Sciences,Goettingen, Germany (1)
Cedars-Sinai Medical Center (1)
Cedars-Sinai, Neurosurgery - Pavilion, 127 S San Vicente Blvd #A6600, Los Angeles, CA, 90048 (1)
Center for Proteomics and Metabolomics; Leiden University Medical Center; 2333 ZA Leiden, The Netherlands (1)
Department of Biological Sciences, KAIST (1)
Department of Biological Sciences, University of Illinois at Chicago (1)
Department of Biomedicine, Aarhus University, Arhus, Denmark (1)
Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Kocaeli, Turkey (1)
Department of Molecular Medicine The Scripps Research Institute (1)
Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI, USA Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA (1)
Department of Ophthalmology, University of California, Irvine, CA 92697 (1)
Department of Ophthalmology, Yongin Severance Hospital, Yonsei University College of Medicine, Republic of Korea (1)
Departments of 1Neurobiology and 2Ophthalmology, Duke University School of Medicine, Durham, NC, USA (1)
Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children’s Hospital, Jackson Health System, Miami, FL, USA. (1)
Duke University Eye Center (1)
EDyP (1)
Eberhard Karls University Tübingen, Institute for Ophthalmic Research (1)
Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden (1)
General Botany, Matthias-Schleiden-Institut, Friedrich-Schiller University Jena Am Planetarium 1, 07743 Jena, Germany (1)

IsPrivate

False (3)

Classification

bacteria (4)
fungi (3)

Study type

Transcription profiling by array (181)
ChIP-seq (125)
RNA-seq of coding RNA (62)
ChIP-chip by tiling array (11)
RNA-seq of coding RNA from single cells (10)
Comparative genomic hybridization by array (9)
Spatial transcriptomics by high-throughput sequencing (6)
RNA-seq of non coding RNA (6)
ChIP-chip by array (4)
Unknown experiment type (3)
High-throughput sequencing (2)
Animal - High-throughput sequencing (2)
Genotyping by array (2)
ATAC-seq (2)
Other (2)
DNA-seq (2)
Transcription profiling by SAGE (1)
Baseline (1)
Animal - Single-cell sequencing (1)
Cell line - One-color microarray (1)
Bisulfite-seq (1)
MicroRNA profiling by array (1)
Methylation profiling by array (1)
Genotyping by high throughput sequencing (1)
RNA-seq of total RNA (1)

Release Date

2022 (447)
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2004 (33)
2002 (23)
2003 (18)
2000 (14)
1999 (11)
2001 (9)
1998 (7)
1997 (4)

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The Bardet-Biedl protein Bbs1 controls photoreceptor outer segment protein and lipid composition

Summary

Primary cilia are key sensory organelles whose dysfunction leads to ciliopathy disorders such as Bardet-Biedl syndrome (BBS). Retinal degeneration is common in ciliopathies, since the outer segments (OSs) of photoreceptors are highly specialized primary cilia. BBS...

2022-02-18 | MTBLS4013 | MetaboLights

Effective transplantation of photoreceptor precursor cells selected via cell surface antigen expression.

Microarray analysis of postnatal NrlGFP-expressing rod photoreceptor precursors. NrlGFP positive versus NrlGFP negative at postnatal day 4

ORGANISM(S): Mus musculus

2013-06-07 | E-MEXP-3922 | 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

The orphan nuclear hormone receptor ERR-beta controls rod photoreceptor survival.

Mutation of rod photoreceptor-enriched transcription factors is a major cause of inherited blindness. We identified the orphan nuclear hormone receptor ERRÎ² as selectively expressed in rod photoreceptors. Overexpression of ERRÎ² induces expression of rod-specific genes in retinas of both wildtype ...

ORGANISM(S): Mus musculus

2010-07-30 | E-GEOD-21944 | biostudies-arrayexpress

Photoreceptor precursors derived from 3D cultures of embryonic stem cells mature and integrate in degenerate retina

To isolate photoreceptor precursors fit for transplantation, we adapted a 3D differentiation protocol that generates neuroretina from mouse ES cells. We used an adeno-associated viral vector (pseudotype2/9)carrying a GFP reporter under the control of a Rhodopsin promoter (AAV2/9.Rhop.GFP)to select r...

ORGANISM(S): Mus musculus

2013-07-17 | E-MEXP-3921 | biostudies-arrayexpress

Transcription profiling of Drosophila photoreceptor cells by

The method of mRNA tagging was recently developed to isolate mRNA population from muscle tissues in Caenohabditis elegans. This method utilizes a FLAG-tagged poly(A)-binding protein (PABP), which can bind to poly(A)-tail of eukaryotic mRNA. Thus, the mRNA population from specific tissue, in which FL...

ORGANISM(S): Drosophila melanogaster

2008-06-12 | E-GEOD-1790 | biostudies-arrayexpress

Single cell RNA-seq of isolated human foetal L/M-opsin cone photoreceptor populations labelled using the AAV2/9.pR2.1.GFP reporter

Human cone photoreceptors represent a rare cell population of the human retina and are largely outnumbered by other retinal cell types. Despite their rarity, cone photoreceptors are critical for optimal daylight vision and their loss has the greatest impact on sight during the progression of retinal...

ORGANISM(S): Homo sapiens

2018-04-20 | E-MTAB-6058 | biostudies-arrayexpress

LC-MSMS on mouse retina to investigate photoreceptor degeneration

Intraocular anti-VEGFA injections are frequently used to counteract neovascularization in diseases such as the neovascular (wet) form of age-related macular degeneration (AMD) or proliferative diabetic retinopathy. However, in the clinical context, patients with atrophic (dry) and wet AMD in the sam...

ORGANISM(S): Mus musculus (Mouse)

2026-06-15 | PXD066263 | Pride

Transcription profiling of mouse retina with ectopic expression of NR2E3 in Nrl-/- animals reveals in vivo function of NR2E3 in establishing photoreceptor identity during mammalian retinal development

Rod and cone photoreceptors in mammalian retina are generated from common pool(s) of neuroepithelial progenitors. NRL, CRX and NR2E3 are key transcriptional regulators that control photoreceptor differentiation. Mutations in NR2E3, a rod-specific orphan nuclear receptor, lead to loss of rods, incr...

ORGANISM(S): Mus musculus

2008-06-13 | E-GEOD-5338 | biostudies-arrayexpress

RNA-Seq of eye tissues from C57BL/6J background mice at 1.5 h and 9.0 h after light onset

We report RNA-Seq experiments of whole eye tissues from C57BL/6J background mice at 1.5 h and 9.0 h after light onset to better understand photoreceptor phagocytosis Examine ocular tissue from mice at different time points

ORGANISM(S): Mus musculus

2013-08-07 | E-GEOD-48974 | biostudies-arrayexpress

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