Human tau mutations in cerebral organoids induce a progressive dyshomeostasis of cholesterol

Single cell RNA sequencing (drop-seq) data of forebrain organoids carrying pathogenic MAPT R406W and V337M mutations. Organoids were generated from 5 heterozygous donor lines (two R406W lines and three V337M lines) and respective CRISPR-corrected isogenic controls. Organoids were also generated from one homozygous R406W donor line. Single-cell sequencing was performed at 1, 2, 3, 4, 6 and 8 months of organoid maturation., Single-cell transcriptomes were obtained using drop-seq (Macosko et al., 2015, https://doi.org/10.1016/j.cell.2015.05.002).
Counts matrices were generated using the Drop-seq tools package (Macosko et al. 2015), with full details available online (https://github.com/broadinstitute/Drop-seq/files/2425535/Drop-seqAlignmentCookbookv1.2Jan2016.pdf). Briefly, raw reads were converted to BAM files, cell barcodes and UMIs were extracted, and low-quality reads were removed. Adapter sequences and polyA tails were trimmed, and reads were converted to Fastq for STAR alignment (STAR version 2.6). Mapping to human genome (hg19 build) was performed with default settings. Reads mapped to exons were kept and tagged with gene names, beads synthesis errors were corrected, and a digital gene expression matrix was extracted from the aligned library. We extracted data from twice as many cell barcodes as the number of cells targeted (NUM_CORE_BARCODES = 2x # targeted cells).
Downstream analysis was performed ..., The package Seurat (https://satijalab.org/seurat) in R is required to read the FB1.seurat file