Photoreceptors - OmicsDI

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Organisms

Mus musculus (205)
Homo sapiens (67)
Danio rerio (32)
Arabidopsis thaliana (32)
Drosophila melanogaster (23)
Rattus norvegicus (6)
Gallus gallus (5)
Ictidomys tridecemlineatus (4)
Neurospora crassa (3)
Chlorocebus sabaeus (2)
Phaeodactylum tricornutum (2)
Anableps anableps (2)
Fusarium fujikuroi (2)
synthetic construct (2)
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Rhyparobia maderae (1)
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Mustela putorius furo (1)
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Anolis sagrei (1)
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unidentified (1)
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Repository

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geo (407)
biostudies-arrayexpress (125)
pride (43)
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Tissue

Retina (13)
Retinal rod (4)
Brain (3)
Cell culture (3)
Retinal rod cell (3)
Eye (2)
Photoreceptor cell (2)
Photoreceptor layer of retina (2)
Plant cell (2)
Vitreous humor (2)
Early embryonic cell (1)
Egg (1)
Embryo (1)
Kidney (1)
Layer of retina (1)
Neural retina (1)
Photosynthetic cell (1)
Primary cell (1)
R1 photoreceptor cell (1)
Retinal cell (1)
Retinal cone cell (1)
Retrocerebral complex (1)
Seedling (1)
Stem cell (1)
Stem cell differentiation (1)
Whole body (1)

Disease

Disease free (4)
Bardet-Biedl syndrome 1 (2)
Age related macular degeneration 1 (1)
Night blindness (1)
Retinal degeneration (1)
Retinal disease (1)
Retinitis (1)
Retinitis pigmentosa (1)
Retinitis pigmentosa 11 (1)

Technology Type

Mass Spectrometry (43)
Shotgun proteomics (23)
Bottom-up proteomics (7)
Data-independent acquisition (6)
Affinity purification coupled with mass spectrometry proteomics (5)
Chemical cross-linking coupled with mass spectrometry proteomics (3)
Data-dependent acquisition (3)
Gel-based experiment (3)
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HDMSE (2)
SRM/MRM (2)
Mass spectrometry (1)
Mass spectrometry assay (1)
Top-down proteomics (1)

Instrument Platform

GC MS (4)
LTQ Orbitrap Velos (4)
Illumina NovaSeq 6000 (3)
Orbitrap Exploris 480 (3)
GC-MS (3)
Orbitrap Fusion Lumos (3)
Illumina HiSeq 2500 (2)
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BD FACSARIA III (1)
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418 [Affymetrix] (1)
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Illumina HiSeq 4000 (1)
Agilent 7890A GC with 5975C inert XL MSD (1)
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Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - alternating - reverse phase (1)

Publication Date

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2010 (30)
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2016 (28)
2014 (28)
2015 (27)
2017 (26)
2019 (22)
2018 (19)
2012 (19)
2009 (17)
2008 (15)
2007 (12)
2013 (7)
2006 (4)
2005 (3)
2003 (1)

UNIPROT ID/AC

P92973 (1)
Q6R0H1 (1)
Q8L500 (1)
Q93WK5 (1)
Q94BT6 (1)
Q9LKL2 (1)
Q9SQI2 (1)

CHEBI ID

CHEBI:33699 (1)
CHEBI:35222 (1)
CHEBI:36080 (1)
CHEBI:132542 (1)
CHEBI:132579 (1)
CHEBI:13389 (1)
CHEBI:134242 (1)
CHEBI:134487 (1)
CHEBI:134587 (1)
CHEBI:137552 (1)
CHEBI:137590 (1)
CHEBI:140940 (1)
CHEBI:140946 (1)
CHEBI:140951 (1)
CHEBI:156118 (1)
CHEBI:16113 (1)
CHEBI:16238 (1)
CHEBI:16474 (1)
CHEBI:16761 (1)
CHEBI:16908 (1)
CHEBI:17239 (1)
CHEBI:18075 (1)
CHEBI:183249 (1)
CHEBI:183798 (1)
CHEBI:183799 (1)
CHEBI:183800 (1)
CHEBI:183804 (1)
CHEBI:184023 (1)
CHEBI:25523 (1)
CHEBI:64431 (1)

Metabolite Name

ADP (1)
AcCa (12:0) (1)
Argininosuccinic acid (1)
CDP (1)
CE (16:1) (1)
CE (18:0) (1)
CE (18:1) (1)
CE (18:2) (1)
CE (20:2) (1)
CE (20:4) (1)
Cer (d34:0)a.(d18:0/16:0) (1)
Cer (d34:0)b.(d16:0/18:0) (1)
Cer (d40:0).(d18:0/22:0) (1)
Cer (d40:1)b.(d18:1/22:0) (1)
Cer (d42:1)a.(d18:0/24:1) (1)
Cer (d42:1)b.(d18:1/24:0) (1)
Cer (d42:2)b.(d18:1/24:1) (1)
Cer (d44:2)a.(d18:1/26:1) (1)
Cer (d44:2)b.(d20:1/24:1) (1)
Cer (m34:0).(m18:0/16:0) (1)
Cer (m34:2).(m18:2/16:0) (1)
Cer (m36:2).(m18:2/18:0) (1)
Cer (m38:0).(m18:0/20:0) (1)
Cer (m38:2)b.(m18:2/20:0) (1)
Cholesterol.-H2O (1)
DAG (32:0).(30:0/FA16:0) (1)
DAG (36:2).(36:2/FA18:1) (1)
DAG (38:5).(38:5/FA18:1) (1)
FA (14:0) (1)
FA (17:1) (1)

First Public Date

2014 (67)
2026 (58)
2025 (58)
2023 (48)
2024 (42)
2022 (38)
2021 (38)
2020 (32)
2017 (26)
2019 (24)
2018 (18)
2016 (16)
2015 (10)
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)
Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China (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)
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)
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 Biophysical Chemistry Department of Clinical Chemistry, University Medical Center Goettingen (1)
Bioanalytical Mass Spectrometry Group,Max-Planck-Institute for Multidisciplinary Sciences,Goettingen, Germany (1)
Biotechnology Laboratory, Department of Biological Applications and Technologies, Universityof Ioannina, 45110 Ioannina, Greece (1)
Center for Proteomics and Metabolomics; Leiden University Medical Center; 2333 ZA Leiden, The Netherlands (1)
Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, Indiana 47907, USA (1)
Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands (1)
Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Kocaeli, Turkey (1)
Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo (1)
Departments of 1Neurobiology and 2Ophthalmology, Duke University School of Medicine, Durham, NC, USA (1)
Duke University Eye Center (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)
Group “Retinal degeneration and regeneration” Department of Ophthalmology University of Lausanne Hôpital Ophtalmique Jules-Gonin Fundamental research center 15 av. de France 1004 Lausanne Switzerland (1)
INGEBI-CONICET, Buenos Aires, Argentina (1)
Institute of Medical Genetics, Bachmann-Lab, University of Zurich (1)
Institute of Medical Genetics, Bachmann-Lab, University of Zurich, Switzerland (1)
Lab for Retinal Cell Biology Dept. Ophthalmology USZ / UZH University of Zurich (1)
Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, UMR7178, Strasbourg, France (1)
Laboratory for Retinal Cell Biology, Departhment of Ophtalmology, University Hospital Zurich, University Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland (1)
Laboratory of Neural Development and Regeneration, CIBIO Department - University of Trento Via Sommarive 9, 38123 Trento, ITALY Centre for Medical Sciences - CISMed University of Trento Via S. Maria Maddalena 1, 38122 Trento, Italy (1)
Max F.Perutz Laboratories (MFPL), University of Vienna; MFPL Mass Spectrometry Facility (1)
Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Göttingen, Germany University Medical Center Göttingen, Department of Clinical Chemistry, Bioanalytics Group, Göttingen, Germany (1)

IsPrivate

False (3)

Classification

fungi (2)
bacteria (1)

Modification

4x(2)H labeled dimethylated L-lysine (2)

Study type

Transcription profiling by array (88)
RNA-seq of coding RNA (23)
ChIP-seq (4)
RNA-seq of non coding RNA (3)
RNA-seq of coding RNA from single cells (2)
Baseline (1)
Unknown experiment type (1)
ChIP-chip by tiling array (1)
Cell line - One-color microarray (1)
Animal - High-throughput sequencing (1)

Release Date

2022 (350)
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2015 (195)
2016 (192)
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Transcriptomic profiling of adult zebrafish photoreceptors

PRJNA779419 | ENA

A mouse photoreceptor proteome resource

To enrich mouse rod and cone photoreceptors for mass spectrometric analysis, we optimized our previously established trituration-based fluorescence-activated cell sorting (FACS) strategy (see Lux et al., 2024 for details; PMID: 38481472). For quantitative mass spectrometry, we utilized an ion mobili...

ORGANISM(S): Mus musculus (Mouse)

2025-12-08 | PXD066755 | Pride

Differential proteomes in the vitreous of mice with a chronic hypoxic response in photoreceptors

Reduced oxygenation of photoreceptors and the RPE in the ageing eye may be a risk factor for the development of both neovascular and dry AMD. Chronic activation of the molecular response to hypoxia in RPE or photoreceptors leads to retinal degeneration that depends on hypoxia inducible transcription...

ORGANISM(S): Mus musculus (Mouse)

2019-06-12 | PXD008911 | Pride

Retinal degeneration Vitreous Cones Rods Hypoxic response Amd Shot-gun proteomics

CLK and CYC CUT&RUN in aging Drosophila photoreceptors

PRJNA1064159 | ENA

Identification of genes with enriched expression in early developing mouse cone photoreceptors

PRJNA547437 | ENA

Transcriptome dynamics of developing photoreceptors in 3-D retina cultures recapitulates temporal sequence of human cone and rod differentiation revealing cell surface markers and gene networks

To define molecular mechanisms underlying rod and cone differentiation, we generated H9 human embryonic stem cell line carrying a GFP reporter that is controlled by the promoter of cone-rod homeobox (CRX) gene, the first known marker of post-mitotic photoreceptor precursors. CRXp-GFP reporter in H9 ...

ORGANISM(S): Homo sapiens

2015-08-03 | E-GEOD-67645 | biostudies-arrayexpress

Epigenetic and transcriptional changes in aging mouse rod photoreceptors [WGBS]

PRJNA556668 | ENA

Photostimulation Promotes Maturation of Human Stem Cell-Derived Photoreceptors

PRJNA1277328 | ENA

Epigenetic and transcriptional changes in aging mouse rod photoreceptors [CUT&RUN]

PRJNA573908 | ENA

Gene expression profiling in ninaE wild type and ninaE G69D/+ Drosophila photoreceptors

PRJNA767700 | ENA

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