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SRX5399158: GSM3612831: ctrl; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 8.9M spots, 1.2G bases, 619.1Mb downloads

Submitted by: NCBI (GEO)
Study: Single cell RNA-seq identifies a unique microglia subtype associated with retinal degeneration
show Abstracthide Abstract
In many forms of retinal degenerative diseases in human, microglia relocate to and accumulate in the subretinal space. However, the roles of microglia in retinal degeneration are poorly understood. By leveraging single cell RNA-seq, we identified a distinct microglia subtype in the subretinal space. These microglia underwent transcriptional reprogramming characterized by reduced expression of homeostatic checkpoint genes and upregulation of injury-responsive genes. Importantly, this transition is associated with protection of the retinal pigment epithelium from damage caused by disease. Therefore, our data demonstrated microglial heterogeneity in retinal degeneration and may provide important implications for developing new strategies to prevent loss of vision. Overall design: Transcriptional profiling of Cx3cr1+ single cells from the mouse model of light-induced retinal degeneration with matched control, generated from single cell RNA-sequencing of over 10,000 cells.
Sample: ctrl
SAMN10968395 • SRS4386075 • All experiments • All runs
Organism: Mus musculus
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: Isoalted retinas from 5 to 8 mice per group were pooled and digested in 1.5 mg/ml collagenase A and 0.4 mg/ml DNase I (Roche) for 30 min at 37 °C to generate single cell suspensions. Cells were stained with PE before FACS sorting. Live Cx3cr1YFP+ cells were sorted by FACS Single Cell RNA libraries were prepared using standard 10x Genomics 3' end library protocols
Experiment attributes:
GEO Accession: GSM3612831
Runs: 1 run, 8.9M spots, 1.2G bases, 619.1Mb
Run# of Spots# of BasesSizePublished


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