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Series GSE246183 Query DataSets for GSE246183
Status Public on Nov 27, 2023
Title Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Neurodegeneration is a protracted process involving progressive changes in myriad cell types that ultimately result in the death of vulnerable neuronal populations. To dissect how individual cell types within a heterogeneous tissue contribute to the pathogenesis and progression of a neurodegenerative disorder, we performed longitudinal single-nucleus RNA sequencing of mouse and human spinocerebellar ataxia type 1 (SCA1) cerebellar tissue, establishing continuous dynamic trajectories of each cell population. Importantly, we defined the precise transcriptional changes that precede loss of Purkinje cells and, for the first time, identified robust early transcriptional dysregulation in unipolar brush cells and oligodendroglia. Finally, we applied a deep learning method to predict disease state accurately and identified specific features that enable accurate distinction of wild-type and SCA1 cells. Together, this work reveals new roles for diverse cerebellar cell types in SCA1 and provides a generalizable analysis framework for studying neurodegeneration.
Overall design Single-nucleus RNA-sequencing was performed of control and SCA1 human post-mortem cerebellar cortex tissues and SCA1 knock-in (KI; Atxn1 154Q/2Q) and wild-type (WT) littermate control mice to examine the complex and dynamic interplay between diverse cell populations in the SCA1 cerebellum over time.
Contributor(s) Tejwani L, Ravindra N, Lee C, van Dijk D, Lim J
Citation(s) 38016472
Submission date Oct 25, 2023
Last update date Jan 05, 2024
Contact name Changwoo Lee
Organization name Yale University
Department Neuroscience
Lab Janghoo Lim
Street address 295 Congress
City New Haven
State/province CT
ZIP/Postal code 06510
Country USA
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (54)
GSM7864602 WT_5W_1
GSM7864603 WT_5W_2
GSM7864604 WT_5W_3
BioProject PRJNA1032006

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Supplementary file Size Download File type/resource
GSE246183_211027_mouse.h5ad.gz 3.3 Gb (ftp)(http) H5AD
GSE246183_230502_human_ctype.h5ad.gz 3.2 Gb (ftp)(http) H5AD
GSE246183_Table_S1.xlsx 20.4 Kb (ftp)(http) XLSX
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