Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Single cell RNAseq of 12-week old AKIMBA versus WT mouse retina

ABSTRACT: Single-cell RNA sequencing was performed on retinal tissue from 12-week-old wild-type and Akimba (Ins2AkitaxVEGF+/-) mice, which are known to replicate features of clinical diabetic retinopathy. The aim of this study was to provide deeper insight into the complex network of molecular and cellular changes that underlie diabetic retinopathy by measuring the transcriptional changes that occur in the different cellular compartments of the degenerating diabetic mouse retina. Retinas (n=4 for Akimba, n=2 for wild-type) were isolated in ice-cold Dulbecco’s Modified Eagle Medium. After rinsing with Dulbecco’s Phosphate-Buffered Saline containing 2% fetal bovine serum, each retina was incubated with 1mL digestion buffer (2mg/mL collagenase-P, 200U/mL DNAse-I (Sigma-Aldrich) in M199 medium (Life Technologies) at 37°C for 10min. Retinal tissue was further dissociated by trituration and the suspension was filtered through a 40µm cell strainer and centrifuged for 5min at 300xg (4°C). Pooled retinal single-cell suspensions from wild-type and Akimba were counted on a Luna-FL Cell Counter (Logos Biosystems) and libraries were prepared with the Chromium Single-cell 3’ V2 Chemistry Library Kit, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics) aiming for 5000 cells per library. Barcoded libraries were sequenced on an Illumina HiSeq4000 in 25-8-98 paired-end configuration. The transcriptome data for 9474 retinal cells were analysed, yielding 15 clusters corresponding to eight distinct retinal cell types.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Michael Porcu

PROVIDER: E-MTAB-9061 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Single-cell transcriptome analysis of the Akimba mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy.

Van Hove Inge I De Groef Lies L Boeckx Bram B Modave Elodie E Hu Tjing-Tjing TT Beets Karen K Etienne Isabelle I Van Bergen Tine T Lambrechts Diether D Moons Lieve L Feyen Jean H M JHM Porcu Michaël M

Diabetologia 20200730 10

<h4>Aims/hypothesis</h4>Diabetic retinopathy is a common complication of diabetes and a leading cause of visual impairment and blindness. Despite recent advances, our understanding of its pathophysiology remains incomplete. The aim of this study was to provide deeper insight into the complex network of molecular and cellular changes that underlie diabetic retinopathy by systematically mapping the transcriptional changes that occur in the different cellular compartments of the degenerating diabet ...[more]

PMID: 32734440

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Dataset Information

Single cell RNAseq of 12-week old AKIMBA versus WT mouse retina

Publications

Single-cell transcriptome analysis of the Akimba mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy.

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