DOI: 10.1038/s41586-025-09520-y
This repository contains the main analysis code and links to raw and processed datasets, and relevant analysis pipelines, to reproduce (or extend on) results from our paper.
- Clone the repository:
git clone git@github.com:djunamay/ABCA7lof2.git
cd ABCA7lof2-
Raw and processed data are available via Synapse, OSF, or Gene Expression Omnibus.
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The single-cell atlas can be interactively explored through the Broad Single Cell Portal.
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See this table for a specific overview of data availability.
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Follow the READMEs below to get to specific code.
| Analysis | Description | Go to Code and Readme |
|---|---|---|
| Human postmortem - snRNAseq processing | Process raw fastq files from single-nucleus RNA sequencing of human postmortem samples, including quality control and preprocessing steps. | → |
| Human postmortem - sample swap analysis | Perform sample-swap checks. | → |
| Human postmortem - snRNAseq stats | Compute gene- and pathway-level statistics from snRNAseq data. | → |
| Human postmortem - snRNAseq gene-pathway partitioning | Evaluate and apply graph partitioning algorithms to gene and pathway-level statistics from snRNAseq data. | → |
| Human postmortem - snRNAseq ala1527gly | Analysze snRNAseq data from ROSMAP study participants with the ALA1527GLY variant. | → |
| induced-neurons - LCMS | Analyze lipidomic profiles from iPSC-derived neurons using Liquid Chromatography-Mass Spectrometry (LCMS). | → |
| induced-neurons - mRNA | Analyze mRNA datasets from iPSC-derived neurons. | → |
| induced-neurons - O2 consumption rates | Analyze oxygen consumption rates in iPSC neurons | → |
| induced-neurons - membrane potential imaging | Analyze MitoHealth and TMRM dyes from iPSC-derived neurons. | → |
| induced-neurons - CellROX imaging | Analyze CellROX dye from iPSC-derived neurons. | → |
| induced-neurons - Neuronal marker imaging | Show neuroanl marker images from iPSC-derived neurons. | → |
| induced-neurons - ELISAs | Plot Amyloid ELISAs from iPSC-derived neurons. | → |
| cortical organoid - Neuronal marker imaging | Show neuroanl marker images from cortical organoids. | → |
| cortical organoid - ELISAs | Plot Amyloid ELISAs from cortical organoids. | → |
| cortical organoid - ephys | Plot Ephysiological data from cortical organoids. | → |
To install specific environments:
conda create --name envname --file env.txt-
/envs/bulkrna_packages.txtandtrim_env_packages.txtandqtltools_env_packages.txt$\rightarrow$ conda environment for bulk mRNA-seq analysis -
/envs/wgs_env_packages.txt$\rightarrow$ conda environment to access WGS data -
/envs/confocalquant_packages.txt$\rightarrow$ conda environment for confocal image analysis -
/envs/bulkrna_packages.txt$\rightarrow$ conda environment for bulk mRNA-seq analysis -
/envs/scmod_py_packages.txt$\rightarrow$ conda environment for snRNAseq analysis - More Info →