Mouse retinal tissue

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Transcriptomics (2024)
Unknown (443)
Genomics (345)
Proteomics (62)
Metabolomics (41)
Other (4)
Genomic (1)
Methylation profiling (1)
Multiomics (1)

Organisms

Mus musculus (1434)
Homo sapiens (381)
Arabidopsis thaliana (183)
Rattus norvegicus (49)
Danio rerio (23)
Bos taurus (12)
Drosophila melanogaster (11)
Gallus gallus (10)
Sus scrofa (7)
Euphorbia esula (4)
Lepidium sativum (4)
Zea mays (4)
synthetic construct (4)
Pimephales promelas (3)
Pan troglodytes (3)
Rattus rattus (3)
Mycobacterium tuberculosis (3)
Ovis aries (3)
Pseudomonas aeruginosa (3)
Saccharomyces cerevisiae (3)
Capra hircus (2)
Callithrix jacchus (2)
Macaca mulatta (2)
Papio hamadryas (2)
Gasterosteus aculeatus (2)
Ornithorhynchus anatinus (2)
Equus caballus (2)
Daphnia magna (2)
Populus tremula x Populus tremuloides (2)
mouse gut metagenome (2)

Organisms

Mus musculus (116)
Homo sapiens (7)
Canis lupus familiaris (1)

Repository

biostudies-arrayexpress (2137)
ENA (143)
geo (86)
MetaboLights (41)
pride (29)
MassIVE (23)
EGA (15)
jPOST (3)
iProX (2)
PanoramaPublic (2)
dbGaP (1)
GPMDB (1)
PAXDB (1)

Tissue

Retina (11)
Brain (5)
Eye (3)
Retinal pigment epithelium cell (3)
Neural retina (2)
Retinal pigment epithelial cell (2)
R1 photoreceptor cell (1)
Photoreceptor layer of retina (1)
Choroid (1)
Tear (1)
Retinal pigment epithelium (1)
Optic nerve (1)
Retinal pigment epithelium cell line (1)
Vitreous humor (1)
Heart (1)
Whole body (1)
Spleen (1)
Epithelial cell (1)
Kidney (1)
Liver (1)

Disease

Normal (18)
Rheumatoid arthritis (2)
Pre-diabetic (2)
Cancer (2)
Mammary tumor (2)
Ovarian tumor (2)
Early stage liver carcinogenesis (1)
Breast Normal (1)
Hepatomegaly (1)
Unspecified peripheral T-cell lymphoma (1)
Perilobar nephrogenic rest (1)
CUP (1)
Myeloid neoplasm (1)
Embryonic lethal at day 8.5 to 9.5 (1)
Spinal muscular atrophy (1)
MPIN (murine prostatic intraepithelial neoplasia) (1)
Non-metastatic melanoma (1)
Hodgkin lymphoma, mixed cellularity, stage IV (1)
MFC II (1)
Teratozoospermia and infertility (1)
Breast adenocarcinoma (1)
Represent tolerant CD4+ T cells that have not been activated (1)
Retinitis pigmentosa (1)
IRAK-4 Q293X mutation (1)
Fibrosis (1)
ARR1-SRDX (1)
Hyperglycaemic (1)
Pre-diabetic, non-obese diabetic (NOD) (1)
Familial adenomatous polyposis (FAP) (1)
Spinal muscular atrophy (NCI Metathesaurus C0026847) has DiseaseStaging postsymptomatic (1)

Technology Type

Mass Spectrometry (29)
Mass spectrometry assay (22)
Mass spectrometry (18)
Shotgun proteomics (15)
Bottom-up proteomics (5)
SWATH MS (3)
Data-dependent acquisition (3)
Affinity purification coupled with mass spectrometry proteomics (3)
Data-independent acquisition (2)
Top-down proteomics (2)
ILLUMINA, Illumina HiSeq 4000, Illumina HiSeq 2500 (1)
Illumina HiSeq 2500, ILLUMINA (1)
Illumina MiSeq (1)
NMR spectroscopy (1)

Instrument Platform

Illumina NovaSeq 6000 (83)
Illumina HiSeq 4000 (50)
Illumina HiSeq 2500 (48)
Illumina HiSeq 2000 (47)
NextSeq 500 (38)
NextSeq 550 (28)
NextSeq 2000 (15)
Axon GenePix 4000A scanning hardware (14)
Scanning hardware (14)
Illumina MiSeq (12)
G2565BA DNA microarray scanner [Agilent] (5)
NA (5)
Illumina HiSeq 1500 (5)
GenePix 4000A [Axon Instruments] (4)
Illumina NovaSeq X (4)
G2565AA DNA microarray scanner [Agilent] (3)
Illumina Genome Analyzer IIx (3)
Axon- GenePix4000B (3)
ScanArray Express HT [PerkinElmer] (3)
Illumina Genome Analyzer II (3)
Flow Cytometer (3)
Illumina HiSeq 3000 (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)
Thermomixer (2)
Chromium 10x (2)
10x Chromium (2)
G2565BA DNA microarray scanner (2)
Microcentrifuge (2)
Agilent DNA Microarray Scanner Model #G2565BA (2)
BD FACS Aria III (2)

Publication Date

2014 (233)
2015 (230)
2013 (217)
2012 (198)
2010 (194)
2011 (169)
2016 (150)
2009 (95)
2007 (89)
2008 (86)
2005 (76)
2026 (72)
2025 (68)
2021 (62)
2006 (62)
2022 (58)
2023 (57)
2024 (49)
2020 (42)
2017 (33)
2019 (28)
2004 (26)
2018 (25)
2003 (2)
2002 (2)

UNIPROT ID/AC

CAD10_MOUSE (1)
KCNA2_MOUSE (1)
DLGP2_MOUSE (1)
PPR29_MOUSE (1)
CP46A_MOUSE (1)
GBRA3_MOUSE (1)
K1549_MOUSE (1)
CLD11_MOUSE (1)
HCN1_MOUSE (1)
KCIP4_MOUSE (1)
GRIA1_MOUSE (1)
TSN2_MOUSE (1)
ST32C_MOUSE (1)
GD1L1_MOUSE (1)
ATCAY_MOUSE (1)
DGKB_MOUSE (1)
GABR1_MOUSE (1)
SC6A1_MOUSE (1)
CTND2_MOUSE (1)
NEGR1_MOUSE (1)
HECAM_MOUSE (1)
SHAN2_MOUSE (1)
F169A_MOUSE (1)
RB39B_MOUSE (1)
GRIA3_MOUSE (1)
ASTN1_MOUSE (1)
CNTP2_MOUSE (1)
UN13A_MOUSE (1)
NFASC_MOUSE (1)
BRSK2_MOUSE (1)

CHEBI ID

CHEBI:26271 (7)
CHEBI:18012 (7)
CHEBI:17822 (6)
CHEBI:25094 (6)
CHEBI:18237 (6)
CHEBI:22660 (6)
CHEBI:22653 (6)
CHEBI:18186 (6)
CHEBI:16811 (6)
CHEBI:28300 (6)
CHEBI:18257 (6)
CHEBI:25017 (6)
CHEBI:15428 (6)
CHEBI:6650 (6)
CHEBI:28044 (6)
CHEBI:37024 (6)
CHEBI:27266 (6)
CHEBI:15891 (6)
CHEBI:16449 (6)
CHEBI:16919 (6)
CHEBI:27897 (6)
CHEBI:15354 (6)
CHEBI:30769 (6)
CHEBI:26986 (5)
CHEBI:24898 (5)
CHEBI:16958 (5)
CHEBI:16610 (5)
CHEBI:16335 (5)
CHEBI:18211 (5)
CHEBI:24813 (5)

Metabolite Name

Retinal (13)
Taurine (12)
Adenosine (12)
Riboflavin (12)
Creatine (12)
Citrulline (11)
Serotonin (11)
Pyridoxal (11)
Uridine (11)
Creatinine (11)
ADP (10)
Succinic acid (10)
Pyridoxine (10)
Spermidine (10)
Xanthine (10)
Inosine (10)
Hypoxanthine (10)
Anserine (9)
Hexaethylene glycol (9)
Ergothioneine (9)
Allantoin (9)
N4-Acetylcytidine (9)
Taurocholic acid (9)
Sebacic acid (9)
Oleamide (9)
Sphinganine (9)
Cytosine (9)
L-Glutamine (9)
Guanosine (9)
Glycerophosphocholine (9)

First Public Date

2022 (27)
2025 (20)
2026 (16)
2024 (14)
2020 (12)
2021 (11)
2014 (11)
2019 (9)
2023 (8)
2017 (5)
2018 (3)
2016 (3)
2015 (3)
2013 (1)

Study type

Transcription profiling by array (1284)
RNA-seq of coding RNA (306)
ChIP-seq (133)
RNA-seq of coding RNA from single cells (76)
Methylation profiling by high throughput sequencing (38)
Unknown experiment type (37)
RNA-seq of non coding RNA (35)
Other (26)
Comparative genomic hybridization by array (22)
ChIP-chip by array (18)
ChIP-chip by tiling array (15)
DNA-seq (14)
Animal - High-throughput sequencing (12)
RNA-seq of total RNA (12)
MicroRNA profiling by array (11)
Methylation profiling by array (10)
Transcription profiling by RT-PCR (9)
Spatial transcriptomics by high-throughput sequencing (8)
Animal - Single-cell sequencing (6)
Genotyping by array (6)
ATAC-seq (6)
ScATAC-seq (5)
Single nucleus RNA sequencing (5)
Cell line - High-throughput sequencing (4)
Baseline (3)
Plant - One-color microarray (3)
Transcription profiling by tiling array (3)
Transcription profiling by SAGE (2)
Differential (2)
Human - High-throughput sequencing (2)

Release Date

2014 (255)
2015 (244)
2013 (229)
2012 (205)
2010 (198)
2011 (173)
2016 (167)
2009 (100)
2007 (94)
2025 (91)
2021 (90)
2008 (88)
2020 (86)
2005 (77)
2023 (71)
2006 (64)
2022 (63)
2024 (58)
2017 (51)
2018 (50)
2026 (45)
2019 (45)
2004 (27)
2003 (4)
2002 (2)
1999 (1)
1998 (1)
1997 (1)

Lab affiliation

University of Pittsburgh School of Medicine, Ophthalmology department (1)
Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America (1)
Department of Ophthalmology, Yongin Severance Hospital, Yonsei University College of Medicine, Republic of Korea (1)
Barbara M. Braunger, Institute of Neuroanatomy, University Clinic Hamburg-Eppendorf, Hamburg, Germany (1)
University of Miami Miller School of Medicine, Department of Ophthalmology, Miami Integrative Metabolomics Research Center, Bascom Palmer Eye Institute (McKnight Vision Research Center) (1)
Institute for Ophthalmic Research Centre for Ophthalmology, University of Tübingen, Germany (1)
Montpellier Hospital (1)
Eye & Vison Health, Flinders University School of Medicine Flinders Medical Center Flinders University Australia (1)
Department of Biological Sciences University of Delaware Newark, DE, USA. (1)
UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland. (1)
Bascom Palmer Eye Institute University of Miami (1)
Professor, Diana Davis Spencer Foundation Chair for Glaucoma Research, The Jackson Laboratory (1)
LMU Muenchen (1)
Center for Proteomics and Metabolomics; Leiden University Medical Center; 2333 ZA Leiden, The Netherlands (1)
Novartis Institutes for Biomedical Research, 22 Windsor Street, Cambridge MA 02139, USA (1)
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)
Department of Ophthalmology, University of Cologne (1)
School of Optometry, The Hong Kong Polytechnic University, Hong Kong (1)
Lab for Retinal Cell Biology Dept. Ophthalmology USZ / UZH University of Zurich (1)
School of Optometry, The Hong Kong Polytechnic University,Kowloon, Hong Kong SAR, China (1)
Institute for Ophthalmic Research, University Clinics Tuebingen (1)
Professor, The Jackson Laboratory, Bar Harbor, ME 04609 USA (1)
University of Pennsylvania (1)
Section of Mass Spectrometric Proteomics, University Medical Center Hamburg eppendorf (1)
Aarhus University (1)
Helmholtz Zentrum München, Neuherberg, Germany (1)
Associate Professor, University of Maryland College Park, MD 20742 (1)
Department of Chemistry, Korea University (1)
Associate Professor, Department of Biochemistry and Molecular Medicine, West Virginia University (1)

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Multi-omic responses of mouse liver and skeletal muscle to chronic alcohol drinking

The aim of this study was to define and compare the molecular blueprints of chronic alcohol use in the liver and skeletal muscle using an established pre-clinical mouse model.

2025-12-11 | MTBLS12616 | MetaboLights

Ten Mouse Organs Proteome and Metabolome Atlas from Adult to Aging

The complexity of the aging process, encompassing numerous organs and systems, poses a significant challenge in identifying and targeting key factors that drive age-related decline. The multi-organ synchronous molecular intricacies underlying natural aging remain elusive. Here we presented a data...

2025-08-29 | MTBLS10642 | MetaboLights

Subcutaneous white adipose tissue-derived extracellular vesicle maintains intestinal homeostasis via IgA biosynthesis in aging mice

To identify the potential iWAT-derived adipokines that regulate intestinal IgA biosynthesis, we conducted untargeted metabolomics in the serum of iFR and iSham mice. A total of 214 differential abundant metabolites were identified (log2FC >1 or <-1 and adjusted p-value <0.05) between the...

2025-09-05 | MTBLS12800 | MetaboLights

Mouse retinal tissue study in VEGF-induced hyperpermeability.

The goal of the project is to identify novel therapeutic targets for retinal vascular hyperpermeability. Three condition (Control, VEGF, and Anti-VEGF) sample of mouse retinal tissues were extensively characterized by global proteome profiling.

ORGANISM(S): Mus musculus (Mouse)

2016-03-22 | PXD003656 | Pride

RNAseq analysis of the global retinal transcriptome of rod photoreceptor-specific Dicer1 conditional knockout mice and control littermates

We report RNAseq analysis of the transcriptome of retinas from mature rod-specific Dicer1 cKO mice and control littermates lacking Cre expression in order to better understand changes in gene regulation that could lead to retinal degeneration in cKO mice. Examine retinal transcriptome of 3 biologica...

ORGANISM(S): Mus musculus

2014-08-14 | E-GEOD-55377 | biostudies-arrayexpress

Untargeted Metabolomics of Mouse Platelet Pellets by LC-MS/MS

In this study, platelet pellets were isolated from mouse peripheral blood through gradient centrifugation to obtain high-purity platelet samples. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics was performed to comprehensively profile the global metabolic chan...

2026-08-04 | MTBLS15244 | MetaboLights

Transcription profiling of mouse with retinal detachment and accelerated re-attachment

Retinal detachment is a major cause of blindness due to penetrating trauma and ocular inflammation, and is often observed in many patients following cataract extraction surgery. When the retinal photoreceptors detach from their epithelium, stress signals and apoptotic pathways are initiated that wi...

ORGANISM(S): Mus musculus

2008-06-14 | E-GEOD-5766 | biostudies-arrayexpress

Disruption of the Brain-Spleen Axis Impairs Monocyte-Microglia Communication and Accelerates Disease Progression in a Mouse Model of Amyloidosis

Alzheimer’s disease (AD) is characterized by a prolonged asymptomatic phase before cognitive decline emerges, yet the mechanisms driving symptom onset remain unclear. Here, we hypothesized that the transition from asymptomatic to symptomatic disease is linked to dysfunction of brain–immune communica...

2026-06-01 | MTBLS14615 | MetaboLights

small RNAseq analysis of the global retinal transcriptome of rod photoreceptor-specific Dicer1 conditional knockout mice and control littermates

ORGANISM(S): Mus musculus

2014-08-14 | E-GEOD-55376 | biostudies-arrayexpress

Transcription profiling of human donor-matched retinal and choroidal vascular endothelial cells

Consistent with clinical observations that posterior uveitis frequently involves the retinal vasculature and recent recognition of vascular heterogeneity, we hypothesized that retinal vascular endothelium was a cell population of unique molecular phenotype. Donor-matched cultures of primary retinal ...

ORGANISM(S): Homo sapiens

2008-06-15 | E-GEOD-7850 | biostudies-arrayexpress

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