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Transcriptomic profiling of mouse substantia nigra tissue by RNA-seq

ABSTRACT: Transcriptomic profiling of mouse substantia nigra tissue by RNA-seq

PROVIDER: PRJNA738884 | ENA |

REPOSITORIES: ENA

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Transcriptomic profiling of mouse substantia nigra tissue by RNA-seq

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Project description:We report RNA sequencing results of human substantia nigra and putamen samples from Parkinson's disease patients and controls. Each substantia nigra sample is the result of pooling brain tissue from two individuals with the same , while each putamen sample is the result of pooling brain tissue from three individuals. We found 354 differentially expressed genes (DEGs) in the SN of PD patients compared to age-matched controls, while we observed 261 DEGs in the putamen samples. The top-enriched pathways from the SN were associated with “protein folding” and “neurotransmitter transport”, and the putamen DEGs with “synapse organization”. In summary, our data confirms the key role of protein folding and neuronal degeneration in the pathology of PD, and highlights new genes and pathways that have not yet been explored in the context of PD.

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Project description:Proteomic analysis of human substantia nigra using protein and peptide fractionations strategies coupled to nanoLC-MS/MS

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Project description:Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. In this study, we have developed an optimized protocol to facilitate efficient LCM analysis of FFPE tissue specimens. First, we optimized protein extraction from FFPE tissue by comparing different extraction buffers and investigating the influence of immunohistochemical and haematoxylin & eosin staining on proteins. SDS present in the protein extracts was removed with the SP3 digest method, which was modified to improve protein and peptide recoveries. Using a label-free approach protein expression of microdissected samples was compared to intact tissue sections from substantia nigra to evaluate the efficiency of LCM for the purification of small cell populations. The optimized protocol was used to analyse samples containing as few as ~3,000 cells isolated from the substantia nigra, using FFPE tissue. Replicate samples of 15 healthy donors were analysed in five separate TMT10plex batches, resulting in the quantification of >5,600 protein groups.

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