Spatial transcriptomics reveals genes associated with dysregulated mitochondrial functions and stress signaling in Alzheimer's disease

Published: 5 January 2021| Version 2 | DOI: 10.17632/6s959w2zyr.2
Contributor:
Jose Fernandez Navarro

Description

This is the public data repository for the the work presented in Navarro and Croteau et al. iScience, 2020. https://doi.org/10.1016/j.isci.2020.101556 The repository contains 48 Spatial Tancriptomics (ST) sections (24 of the hippocampus and 24 of the olfactory bulb). The sections were obtained from an Alzheimer´s disease mouse model: 3xAD, 3xPB, 3xPB and WT For each section, we have deposited the following: - H&E file - Matrix of counts (spots inside tissue) - Raw matrix of counts with coordinates file We also included the merged matrices of counts and meta files. The results of the analyses are also present (factor analysis clusters, DE analysis genes, pathways, etc...).

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Steps to reproduce

See Methods sections in the paper. Some tools used are the following: https://github.com/jfnavarro/st_pipeline https://github.com/jfnavarro/st_analysis https://github.com/jfnavarro/AD_POLB_ST https://github.com/jfnavarro/spatial-transcriptome-deconvolution

Institutions

KTH Royal Institute of Technology Gene technology

Categories

Bioinformatics, Neurodegenerative Disorder, Machine Learning, Alzheimer's Disease, Transcriptomics, Spatial Analysis

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