GEO DataSets

(Submitter supplied) Purpose: The purpose of this study was　to use RNA-seq to investigate the molecular mechanisms of damage in the early stages of the response to axonal injury, before the onset of RGC death. Methods: 12-week-old wild-type (WT) mice were used in this study. The experiment group underwent an optic nerve crush (ONC) procedure to induce axonal injury in the right eye, and the control group underwent a sham procedure. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: CSV

(Submitter supplied) We performed RNA-seq analysis on the normal and 6-hour post-ONC retinas from the embryonic day (E) 20, postnatal day (P) 1 and P3 mice to determine the retinal transcriptome profiles. The identified differentially expressed genes (DEGs) could be associated with the degeneration of axonal growth capacity after birth, and axonal regeneration. Subsequent K‐means, GO, KEGG, PPI, and GSEA analysis revealed the biological processes and regulatory pathways involved in the DEGs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

21 Samples

Download data: XLSX

(Submitter supplied) Purpose: This study aims to the downstream transcriptional networks controlled by JUN and DDIT which are critical for RGC death Methods: RNA was isolated from the retinas of wild-type mice and mice deficient in Jun, Ddit3, and both Jun and Ddit3 three days after mechanical optic nerve crush injury (CONC), and was subjected to RNA-sequecing. Results: This study identified downstream transcriptional changes after injury included both neuronal survival and pro-inflammatory signaling that were attenuated to differing degrees by loss of Ddit3, Jun, and Ddit3/Jun. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

38 Samples

Download data: TXT

(Submitter supplied) Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the neurons known as retinal ganglion cells (RGCs). Although distinct in vivo animal models have been used to investigate the mechanisms of both RGC degeneration and reorganization of the retina, there has been little progress in developing efficient strategies for neuroprotection in glaucoma. In the present study, we used transcriptomic profiles of Lister Hooded rats’ retinas 2 weeks after optic nerve crush (ONC) and applied systems biology approaches to better understand the molecular mechanisms by which ONC induced the remodeling of the retinal tissue. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL14745

8 Samples

Download data: TXT

(Submitter supplied) In this study, we performed RNA-seq of injured and FACS-purified RGCs receiving CRISPR-mediated knockout of ATF3, ATF4, CEBPγ or CHOP

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

21 Samples

Download data: TSV

(Submitter supplied) In this study, we profiled epigenetic and transcriptional landscapes in injured RGCs to identify transcription factors driving critical chromatin state and gene expression changes in reponse to injury.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

30 Samples

Download data: TSV, TXT

(Submitter supplied) retinal ganglion cells die after optic nerve injury, either crush or transection. The molecular causesunderlying this degeneration are largely unkwon the purpose of this job is to find which (if any) gene regulation triggers RGC death with the final goal of design neuroprotective protocols Keywords: time course

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS3374

Platform:

GPL1355

35 Samples

Download data: CEL

Temporal analysis of retinas of animals following intraorbital optic nerve transection (IONT) or intraorbital nerve crush (IONC). Optic nerve injury, which is more severe with IONT than IONC, triggers retinal ganglion cell death. Results provide insight into the molecular basis of this degeneration.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, transformed count, 3 protocol, 7 time sets

Platform:

GPL1355

Series:

GSE9918

35 Samples

Download data: CEL

(Submitter supplied) To obtain and analyze early retinal changes at molecular level at 24h after ipsilateral intraorbital nerve radiation injury by gamma knife surgery

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL3535

6 Samples

Download data: CEL

(Submitter supplied) Purpose: The goal of the present study is to provide an independent assessment of the retinal transcriptome signatures of the C57BL/6J (B6) and DBA/2J (D2) mice and to enhance existing microarray datasets for accurately defining the allelic differences in the BXD recombinant inbred strains. Methods: Retinas from both B6 and D2 mice (3 of each) were used for the RNA-seq analysis. Transcriptome features were examined for both strains. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT, XLSX

(Submitter supplied) Purpose: The goals of this study are to identify the transcriptional profile of retinal ganglion cells (RGCs) with the capacity to regenerate an axon, and contrast this profile with the profile of RGCs that cannot regenerate an axon. Methods: See sample pages for protocols for tissue preparation, RNA extraction and purification, library construction and data processing. Results: RNA from the 12 samples was sequenced to an average depth of 42 million reads. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) Purpose: We used RNA sequencing to investigate the effect of acupuncture treatment on retinal transcritome after optic nerve injury Methods: Retinal mRNA profiles of 5-week-old wild-type (WT), optic nerve crush injury (ONC), ONC injury with acupuncture treatment at acupoint GB20 (ONC-F) and ONC injury with acupuncture treatment at acupoint BL1 (ONC-J) mice were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

15 Samples

Download data: XLSX

(Submitter supplied) Retinal ganglion cell (RGC) death is the final consequence of many blinding diseases, where there is considerable variation in the time course and severity of RGC loss. Indeed, this process appears to be influenced by a wide variety of genetic and environmental factors. In this study we explored the genetic basis for differences in ganglion cell death in two inbred strains of mice. We found that RGCs are more susceptible to death following optic nerve crush in C57BL/6J mice (54% survival) than in DBA2/J mice (62% survival). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4234

18 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BAM, TXT, XLS

(Submitter supplied) Retinal ganglion cells (RGCs) convey the major output of information collected from the eye to the brain. Thirty subtypes of RGCs have been identified to date. Here, we analyze 6,225 RGCs (average of 5,000 genes per cell) from right and left eyes by single cell RNA-seq and classify them into 40 subtypes using clustering algorithms. We identify additional subtypes and markers, as well as transcription factors predicted to cooperate in specifying RGC subtypes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: CSV

(Submitter supplied) We constructed the first single cell atlas of the human, porcine and zebrafish ocular compartments and compared inter-species transcriptomic expression data in retinal cell populations. In the non-retinal cell populations, we identified putative adult stem cells present in the iris tissue. We created a disease map of genes involved in eye disorders across cells of posterior and anterior compartments of eye. more...

Organism:

Homo sapiens; Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22475 GPL20301

27 Samples

Download data: CSV

(Submitter supplied) Both brain-resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines, chemokines and neurotrophic factors. To identify additional secreted signalling molecules, we used RNA-seq gene expression profiling to detect changes in the transcriptome of macrophage-lineage cells after acute neural injury in larval zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

12 Samples

Download data: CSV

(Submitter supplied) To further our understanding of how biochemical information flows through cells upon external stimulation, we require single-cell multi-omics methods that concurrently map changes in (phospho)protein levels across signaling networks and the associated gene expression profiles. Here, we present Quantification of RNA and Intracellular Epitopes by sequencing (QuRIE-seq), a droplet-based platform for single-cell RNA and intra- and extracellular (phospho)protein quantification through sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

16 Samples

Download data: MATRIX, TSV, TXT, XLSX