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SRP080004
Rattus norvegicus
4 Downloadable Samples
Illumina Genome Analyzer IIx
Description
We report RNA-Seq experiments of eye and retinal tissues from Rattus Norvegicus Overall design: Examine ocular tissue from Rattus Norvegicus
Publication Title
Receptor MER Tyrosine Kinase Proto-oncogene (MERTK) Is Not Required for Transfer of Bis-retinoids to the Retinal Pigmented Epithelium.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We report RNA-Seq experiments of retinal tissue from Homo Sapiens Overall design: Examine retinal tissue from human
Publication Title
Receptor MER Tyrosine Kinase Proto-oncogene (MERTK) Is Not Required for Transfer of Bis-retinoids to the Retinal Pigmented Epithelium.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 30 Downloadable Samples
- Illumina HiSeq 2500
Description
Photoreceptor degeneration is the central event leading to visual impairment or blindness in most retinal diseases. However, the discovery of safe and effective therapeutic strategies conferring photoreceptor protection remains challenging. A systems pharmacology approach, synergistically targeting distinct cellular pathways could provide an effective strategy for evaluating, preventing or treating retinal dystrophies. Here this concept was investigated using a mouse model of light-induced retinal degeneration. We show that a combination of FDA-approved drugs acting on different G protein-coupled receptors in a synergistic manner could protect retinas against light-induced degeneration when each drug in the combination treatment was administered at a sub-therapeutic dose. Furthermore, transcriptome analyses demonstrated that such combined treatments also preserved patterns of retinal gene expression more characteristic of the normal retina than did single therapies at higher doses. The current study thus supports a new systems pharmacology approach that may extend to other complex neurodegenerative disorders in addition to retinal diseases. Overall design: Male and female Abca4-/-Rdh8-/- at the age of 4- to 6-weeks were used for the current study. All mice were housed and maintained in a 12 h light (=10 lux)/12 h dark cyclic environment in the Animal Resource Center at the School of Medicine, Case Western Reserve University (CWRU). Bright light-induced retinal damage was generated by exposing Abca4-/-Rdh8-/- mice to white light delivered at 10,000 lux (150 W spiral lamp, Commercial Electric) for 30 min. All indicated treatments were administered by intraperitoneal injection 30 min prior to bright light exposure and retinas collected one day later. Single compounds and their tested doses were: 2-Bromo-a-ergocryptine methanesulfonate salt (BRM), metoprolol tartrate (MTP), tamsulosin (TAM), and doxazosin (DOX). Combined treatments were: BRM, MTP and TAM (BMT), or MTP, DOX, and BRM (MDB). Processed data files (linked as series supplementary files): DE_combined.txt; Significant differential expression results from the combined pretreatment experiment. DE_mono.txt; Significant differential expression results from the mono pretreatment experiment. eXpress_counts_combined.txt; Quantitation output from eXpress of effective counts from the combined pretreatment experiment. eXpress_counts_mono.txt; Quantitation output from eXpress of effective counts from the mono pretreatment experiment. eXpress_fpkm_combined.txt; Quantitation output from eXpress of fpkm values from the combined pretreatment experiment. eXpress_fpkm_mono.txt; Quantitation output from eXpress of fpkm values from the mono pretreatment experiment. normalized_fpkm_combined.txt; TMM normalized fpkm values from the combined pretreatment experiment. normalized_fpkm_mono.txt; TMM normalized fpkm values from the mono pretreatment experiment.
Publication Title
Synergistically acting agonists and antagonists of G protein-coupled receptors prevent photoreceptor cell degeneration.
Sample Metadata Fields
Specimen part, Subject, Compound
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
We report RNA-Seq analysis of the transcriptome of retinas and RPE/choroids from Abca4 knockout, Abca4 L541P;A1038V knockin and control wild type mice in order to better understand changes in gene regulation that could lead to retinal pathology in mice with ABCA4 deficiency/defect. Overall design: Retinal and RPE/choroidal mRNA profiles of 30-day-old wild type (WT), Abca4-/- and Abca4L541P;A1038V/L541P;A1038V mice were generated by RNA-Seq, using Illumina Hiseq 2500
Publication Title
Protein misfolding and the pathogenesis of ABCA4-associated retinal degenerations.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
We report the single base pair analysis of the ocular transcriptome from wild type and BC027072 knockout animals. Comparison was analyzed to understand gene expression changes in a mouse model for early onset retinal degeneration which phenocopies a human form of autosomal recessive retinitis pigmentosa Overall design: Eye mRNA profiles were generated from 3 week-old C57BL/6J and BC027072 -/- in triplicate and sequenced using the Illumina HiSeq 2500
Publication Title
Animals deficient in C2Orf71, an autosomal recessive retinitis pigmentosa-associated locus, develop severe early-onset retinal degeneration.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 3 Downloadable Samples
- Illumina HiScanSQ
Description
We report RNAseq analysis of the transcriptome of 3 biological replicates of bovine retina Overall design: Examine retinal transcriptome of 3 biological replicates with tissue collected between 7:00 - 10:00AM
Publication Title
Argonaute high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation reveals a snapshot of miRNA gene regulation in the mammalian retina.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Expression of DREAM in dorsal root ganglia and spinal cord is related to endogenous control mechanisms of acute and chronic pain. In primary sensory trigeminal neurons high levels of endogenous DREAM protein are preferentially localized in the nucleus, suggesting a major transcriptional role. Here, we show that DREAM participates in the control of trigeminal pain perception through the regulation of prodynorphin and BDNF. Furthermore, genome-wide analysis of trigeminal neurons in daDREAM transgenic mice revealed that cathepsin L (CTSL) and the monoglyceride lipase (MGLL) are new DREAM downstream targets and have a role in the regulation of trigeminal nociception.
Publication Title
Transcriptional repressor DREAM regulates trigeminal noxious perception.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We report RNA-Seq experiments of whole eye tissues from A/J, BALB/c, and C57BL/6 background mice. Overall design: Examine ocular tissue from 3 different background mice that display varying rates of retinal degeneration.
Publication Title
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We report RNA-Seq experiments of eye and retinal tissues from WT and RHO KO mice Overall design: Examine ocular tissue from different mouse genotypes
Publication Title
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
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 Overall design: Examine ocular tissue from mice at different time points
Publication Title
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas.
Sample Metadata Fields
Specimen part, Cell line, Subject, Time
View Samples