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Series GSE132229 Query DataSets for GSE132229
Status Public on Jan 24, 2020
Title Comprehensive analysis of a mouse model of spontaneous uveoretinitis using single-cell RNA sequencing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Autoimmune uveoretinitis is a significant cause of visual loss, and mouse models offer unique opportunities to study its disease mechanisms. Aire-/- mice fail to express self-antigens in the thymus, exhibit reduced central tolerance, and develop a spontaneous, chronic, and progressive uveoretinitis. Using single-cell RNA sequencing (scRNA-seq), we characterized wild type and Aire-/- retinas to define, in a comprehensive and unbiased manner, the cell populations and gene expression patterns associated with disease. Based on scRNA-seq, immunostaining, and in situ hybridization, we infer that (i) the dominant effector response in Aire-/- retinas is Th1-driven, (ii) a subset of monocytes convert to either a macrophage/microglia state or a dendritic cell state, (iii) the development of tertiary lymphoid structures constitutes part of the Aire-/- retinal phenotype, (iv) all major resident retinal cell types respond to Interferon gamma by changing their patterns of gene expression, and (v) Muller glia up-regulate specific genes in response to Interferon gamma and may act as antigen presenting cells.
Overall design Single-cell RNAseq of AireKO and age- and sex-matched WT retinas. For AireKO retinas, two replicates for Grade 2 disease and two replicates for Grade 3 disease were used.
Contributor(s) Heng JS, Hackett SF, Stein-O'Brien GL, Winer BL, Williams J, Campochiaro PA, Goff LA, Nathans J
Citation(s) 31843893
Submission date Jun 05, 2019
Last update date Jan 24, 2020
Contact name Jacob S Heng
Organization name Johns Hopkins University School of Medicine
Department Molecular Biology and Genetics
Lab Nathans Lab
Street address 725 North Wolfe Street
City Baltimore
State/province MD
ZIP/Postal code 21210
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (8)
GSM3854512 JH21_WT_retina_scRNAseq_R1
GSM3854513 JH22_AireKO_retina_scRNAseq_R1
GSM3854514 JH31_WT_retina_scRNAseq_R2
BioProject PRJNA546561
SRA SRP200499

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Supplementary file Size Download File type/resource
GSE132229_RAW.tar 178.1 Mb (http)(custom) TAR (of MTX, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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