Mus musculus retina

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Transcriptomics (3509)
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Proteomics (194)
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Unknown (12)
Methylation profiling (9)
Multiomics (2)

Organisms

Mus musculus (3336)
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mouse gut metagenome (3)
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Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (2)
Plasmodium chabaudi chabaudi (2)
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Ornithorhynchus anatinus (2)

Organisms

Mus musculus (744)
Mus musculus musculus (3)
Mus musculus domesticus (1)

Repository

biostudies-arrayexpress (3343)
ENA (750)
geo (673)
pride (95)
MassIVE (56)
MetaboLights (33)
EGA (26)
jPOST (16)
iProX (14)
PanoramaPublic (7)
MetabolomicsWorkbench (4)
GNPS (2)
GPMDB (2)
PAXDB (1)

Tissue

Retina (66)
Brain (9)
Retinal cell (6)
Epithelial cell (5)
Neural retina (5)
Retinal rod cell (4)
Blood (3)
Kidney (3)
Liver (3)
Retinal pigment epithelial cell (3)
Retinal rod (3)
Cell culture (2)
Eye photoreceptor cell (2)
Lung (2)
Primary cell (2)
Retinal pigment epithelium cell (2)
Spleen (2)
Testis (2)
Vitreous humor (2)
Retina (1)
Adrenal gland (1)
Cerebellum (1)
Choroid (1)
Endothelial cell (1)
Extracellular vesicle (1)
Heart (1)
Microglial cell (1)
Muller cell (1)
Optic nerve (1)
Photoreceptor cell (1)

Disease

Normal (23)
Pre-diabetic (3)
Not applicable (3)
Retinitis pigmentosa (3)
Rheumatoid arthritis (2)
Cancer (2)
Mammary tumor (2)
Multiple myeloma (2)
Ovarian tumor (2)
Tumor bearing (1)
Early stage liver carcinogenesis (1)
Breast Normal (1)
Hepatomegaly (1)
Unspecified peripheral T-cell lymphoma (1)
Perilobar nephrogenic rest (1)
CUP (1)
P. berghei ANKA GFP sporozoite's infection (1)
Myeloid neoplasm (1)
Embryonic lethal at day 8.5 to 9.5 (1)
Acute Lymphoblastic Leukaemia (1)
Spinal muscular atrophy (1)
MPIN (murine prostatic intraepithelial neoplasia) (1)
Non-metastatic melanoma (1)
Insulin resistance (1)
Photoreceptor degeneration (1)
Hodgkin lymphoma, mixed cellularity, stage IV (1)
MFC II (1)
Teratozoospermia and infertility (1)
Small cell lung cancer (1)
Represent tolerant CD4+ T cells that have not been activated (1)

Technology Type

Mass Spectrometry (99)
Shotgun proteomics (43)
Bottom-up proteomics (28)
Mass spectrometry (16)
Mass spectrometry assay (16)
Data-dependent acquisition (15)
Data-independent acquisition (14)
Gel-based experiment (6)
Top-down proteomics (5)
SWATH MS (4)
Illumina HiSeq 2500, ILLUMINA (3)
ESI (3)
Illumina HiSeq 2500 (2)
HDMSE (2)
SRM/MRM (2)
ILLUMINA, Illumina HiSeq 4000, Illumina HiSeq 2500 (1)
HiSeq X Ten, ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 2000, Affymetrix SNP 6.0 (1)
ILLUMINA, Illumina Genome Analyzer II, Illumina HiSeq 2000 (1)
Illumina MiSeq (1)
NMR spectroscopy (1)
EI (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
DiaPASEF (1)
Mass spectrometry imaging (1)

Instrument Platform

Illumina NovaSeq 6000 (112)
Illumina HiSeq 2500 (97)
Illumina HiSeq 2000 (97)
NextSeq 500 (88)
Illumina HiSeq 4000 (75)
NextSeq 550 (38)
Illumina MiSeq (30)
NextSeq 2000 (23)
Illumina NovaSeq X (18)
Illumina Genome Analyzer II (16)
Illumina HiSeq 1500 (11)
Scanning hardware (9)
Axon- GenePix4000B (6)
G2565BA DNA microarray scanner [Agilent] (6)
Illumina Genome Analyzer IIx (5)
Illumina HiSeq 1000 (5)
Vortex (4)
DNBSEQ-G400 (4)
Element AVITI (3)
Agilent DNA Microarray Scanner Model #G2565BA (3)
Agilent G2565AA and G2565BA Microarray Scanner (3)
G2565AA DNA microarray scanner [Agilent] (3)
ScanArray Express HT [PerkinElmer] (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)
Chromium 10x (2)
G2565BA DNA microarray scanner (2)
Compute Cluster (2)
Sony SH800 (2)
FS450 (2)

Publication Date

2014 (444)
2015 (394)
2013 (391)
2010 (314)
2012 (307)
2016 (284)
2011 (277)
2026 (176)
2025 (176)
2024 (172)
2008 (146)
2023 (143)
2022 (141)
2021 (138)
2009 (129)
2007 (110)
2020 (105)
2005 (86)
2019 (84)
2017 (78)
2018 (62)
2006 (49)
2004 (29)
2003 (2)
2002 (2)

UNIPROT ID/AC

1433B_MOUSE (1)
1433E_MOUSE (1)
1433F_MOUSE (1)
1433G_MOUSE (1)
1433T_MOUSE (1)
1433Z_MOUSE (1)
2A5A_MOUSE (1)
2A5E_MOUSE (1)
2A5G_MOUSE (1)
2AAA_MOUSE (1)
2ABA_MOUSE (1)
3HIDH_MOUSE (1)
4F2_MOUSE (1)
6PGD_MOUSE (1)
6PGL_MOUSE (1)
AAK1_MOUSE (1)
AATC_MOUSE (1)
AATM_MOUSE (1)
ABCB7_MOUSE (1)
ABCE1_MOUSE (1)
ABD12_MOUSE (1)
ABHD6_MOUSE (1)
ABI1_MOUSE (1)
ABLM1_MOUSE (1)
ABLM2_MOUSE (1)
ABR_MOUSE (1)
ACACA_MOUSE (1)
ACAD9_MOUSE (1)
ACADL_MOUSE (1)
ACADM_MOUSE (1)

CHEBI ID

CHEBI:30769 (6)
CHEBI:18012 (6)
CHEBI:30915 (5)
CHEBI:6650 (5)
CHEBI:16958 (5)
CHEBI:15428 (5)
CHEBI:16449 (5)
CHEBI:15891 (5)
CHEBI:26271 (5)
CHEBI:28300 (5)
CHEBI:18186 (5)
CHEBI:22653 (5)
CHEBI:28044 (5)
CHEBI:18237 (5)
CHEBI:32816 (4)
CHEBI:15843 (4)
CHEBI:15551 (4)
CHEBI:16335 (4)
CHEBI:27897 (4)
CHEBI:15741 (4)
CHEBI:24898 (4)
CHEBI:25017 (4)
CHEBI:27266 (4)
CHEBI:26986 (4)
CHEBI:17268 (4)
CHEBI:22660 (4)
CHEBI:25094 (4)
CHEBI:18257 (4)
CHEBI:17822 (4)
CHEBI:16811 (4)

Metabolite Name

Adenosine (4)
Gamma-aminobutyric acid (3)
Uridine (3)
Beta-alanine (3)
Taurine (3)
Methionine sulfoxide (3)
3-hydroxybutyric acid (3)
ADP (3)
Inosine (3)
Creatine (3)
Myo-inositol (3)
Glycine (3)
Glycerol (3)
FAD (3)
Guanosine (3)
Asparagine (3)
Tryptophan (3)
Isoleucine (3)
Glutamic acid (3)
Caprylic acid (3)
Lactic acid (3)
Alanine (3)
Valeric acid (3)
Taurine (3)
Succinic acid (3)
Malic acid (3)
Fumaric acid (3)
Citric acid (3)
Glucose-1-phosphate (2)
O-phosphoethanolamine (2)

First Public Date

2014 (105)
2025 (98)
2024 (93)
2026 (73)
2022 (70)
2023 (68)
2021 (52)
2020 (46)
2017 (42)
2019 (38)
2018 (23)
2015 (20)
2016 (17)
2013 (5)

Modification

4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (1825)
RNA-seq of coding RNA (518)
ChIP-seq (311)
RNA-seq of coding RNA from single cells (104)
Unknown experiment type (68)
Methylation profiling by high throughput sequencing (65)
ChIP-chip by tiling array (51)
RNA-seq of non coding RNA (47)
Other (45)
Comparative genomic hybridization by array (33)
ChIP-chip by array (32)
DNA-seq (22)
Animal - High-throughput sequencing (21)
RNA-seq of total RNA (21)
Methylation profiling by array (17)
MicroRNA profiling by array (15)
Cell line - High-throughput sequencing (14)
Transcription profiling by RT-PCR (13)
ATAC-seq (12)
CUT&RUN (10)
Spatial transcriptomics by high-throughput sequencing (9)
Animal - Single-cell sequencing (7)
Genotyping by array (7)
ScATAC-seq (7)
Single nucleus RNA sequencing (6)
Proteomic profiling by array (6)
Animal - One-color microarray (5)
MicroRNA profiling by high throughput sequencing (5)
CLIP-seq (4)
RIP-seq (4)

Release Date

2014 (426)
2013 (381)
2015 (368)
2010 (298)
2012 (297)
2011 (260)
2016 (249)
2008 (142)
2009 (124)
2007 (105)
2005 (84)
2021 (78)
2026 (68)
2023 (61)
2020 (61)
2025 (60)
2024 (54)
2022 (47)
2006 (44)
2017 (41)
2019 (38)
2018 (37)
2004 (27)
2003 (2)
2002 (2)
1998 (1)

Lab affiliation

Boston Children's Hospital (4)
Center for Translational Vision Research, Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, 92697, USA; Department of Physiology and Biophysics, Department of Chemistry, Department of Molecular Biology and Biochemistry; University of California, Irvine, Irvine, CA, 92697, USA (3)
LSUHSC Proteomics Core Facility Department of Biochemistry and Molecular Biology LSU Health Sciences Center New Orleans, LA 70112 (2)
Neuroproteomics Group Department of Molecular Neurobiology Max Planck Institute for Multidisciplinary Sciences Hermann-Rein-Str. 3 37075 Goettingen Germany (2)
Proteomic Plateform Necker - SFR Necker - US24 (2)
University of Electronic Science and Technology of China (2)
University of Pennsylvania (2)
Washington University in St. Louis School of Medicine (2)
West Virginia University (2)
1. Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA 2. Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA (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)
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)
Adele Niessen Professor of Ophthalmology Vice Chair for Research FM Kirby Center for Molecular Ophthalmology Scheie Eye Institute University of Pennsylvania (1)
Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine (1)
Associate Professor of Neurology Institute for Cell Engineering Johns Hopkins University School of Medicine (1)
Associate Professor, Department of Biochemistry and Molecular Medicine, West Virginia University (1)
Associate Professor, Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong (1)
Barbara M. Braunger, Institute of Neuroanatomy, University Clinic Hamburg-Eppendorf, Hamburg, Germany (1)
Bascom Palmer Eye Institute University of Miami (1)
Center for Proteomics and Metabolomics; Leiden University Medical Center; 2333 ZA Leiden, The Netherlands (1)
Centre For Eye Research Australia(CERA) (1)
Centre for Heamato-Oncology / Barts Cancer Institute (1)
Department of Biochemistry The LSUHSC Proteomic Core Facility Louisiana State University Health Sciences Center New Orleans, LA 70112 (1)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (1)
Department of Biological Sciences University of Delaware Newark, DE, USA. (1)
Department of Biology, University of Fribourg Chemin du Musée 10, 1700 Fribourg, Switzerland (1)
Department of Biomedicine, Aarhus University, Arhus, Denmark (1)
Department of Cell and Developmental Biology, Neuroscience Graduate Program, Department of Neurology University of Michigan Medical School, Ann Arbor, MI 48109-2200 (1)
Department of Chemistry, Korea University (1)

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Oxygen-induced pathological angiogenesis promotes intense lipid synthesis and remodeling in the retina

The retina is a notable tissue with high metabolic needs which relies on specialized vascular networks to protect the neural retina while maintaining constant supplies of oxygen, nutrients and dietary essential fatty acids. Here we analyzed the lipidome of the mouse retina under healthy and patho...

2023-05-09 | MTBLS6965 | MetaboLights

Functional targeting of PTTG1 in pericytes restores vascular integrity in diabetic retina

Pericyte loss is an early and critical event in the pathogenesis of diabetic retinopathy (DR), yet the molecular mechanisms underlying pericyte dysfunction remain incompletely understood. Using single-cell RNA sequencing, we generated a retinal cellular overview comprising 37,982 cells from diabetic...

2026-03-30 | MTBLS14184 | MetaboLights

Functional targeting of PTTG1 in pericytes restores vascular integrity in diabetic retina

2026-03-27 | MTBLS13544 | MetaboLights

12 weeks control & STZ B6 mice retina & plasma amino acid analysis

Not available

ORGANISM(S): Mus musculus

ST000829 | MetabolomicsWorkbench

Transcription profiling of mouse developing and mature Nrl -/- retina against wild type controls

The rod photoreceptor-specific neural retina leucine zipper protein Nrl is essential for rod differentiation and plays a critical role in regulating gene expression. In the mouse retina, rods account for 97% of the photoreceptors; however, in the absence of Nrl (Nrl-/-), no rods are present and a co...

ORGANISM(S): Mus musculus

2009-10-30 | E-GEOD-8972 | biostudies-arrayexpress

Mus musculus breed:C57BL/6J

Mus musculus raw sequence reads for AGO HITS-CLIP in retina

PRJNA606092 | ENA

Proteomic profiling of embryonic retina to facilitate ocular disease gene discovery

To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefor...

ORGANISM(S): Mus musculus (Mouse)

2023-10-09 | PXD039490 | Pride

Transcription profiling of mouse retina from four genotypes: +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl at P14 and P28

Rorb is essential for rod photoreceptor development in the mouse retina. Using Affymetrix mouse GeneChips, we have generated expression profiles of the +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl retina at P14 and P28. In this dataset, we include the expression data obtained from retina of wt and...

ORGANISM(S): Mus musculus

2009-10-23 | E-GEOD-16585 | biostudies-arrayexpress

Gene regulation in the hyperoxia mouse retina

PURPOSE: Hyperoxia is toxic to photoreceptors, and this toxicity may be important in the progress of retinal dystrophies. This microarray study examines gene expression induced in the C57BL/6J mouse retina by hyperoxia over the 14-day period during which photoreceptors first resist, then succumb to,...

ORGANISM(S): Mus musculus

2010-08-05 | E-GEOD-23437 | biostudies-arrayexpress

Selective knockout of NeuroD1 in the retina and pineal gland

NeuroD1 encodes a basic helix-loop-helix transcription factor involved in the development of neural and endocrine structures. NeuroD1 mRNA is highly abundant in the adult mammalian pineal gland and exhibits a developmental expression pattern similar to the retina. This is consistent with the common ...

ORGANISM(S): Mus musculus

2012-07-25 | E-GEOD-35396 | biostudies-arrayexpress

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