Resources
We believe that open data sharing and collaboration are essential for the advancement of science, and makes the job more fun! Below, we have provided access to our data and protocols that may be useful to the scientific community.
Please feel free to contact us if you have any questions or would like additional information
Data
MAPT V337M organoid single cell data
Our most requested data! This is single cell data from our 2021 Cell paper , where we transcriptomically profile iPSC-derived forebrain organoids with MAPT V337M mutations using single cell and bulk RNA-sequencing.
You can find the raw single cell data on GEO HERE (be sure to check the README for barcode info)
The raw bulk RNAseq data and gene counts are HERE
Alternatively, to make the data easier to use and much more accessible, you can download the processed and annotated Seurat objects from the links below. These files were processed as described in our paper. Please note that due to their size, the data is split by organoid age.
Additionally, all processed files (Gene counts, DEGs, GSEA) from the bulk sequencing can be downloaded HERE
SingleR reference annotation data
The combined scRNAseq data from Polioudakis et al 2019 and Zhang et al 2016, packaged into SingleCellExperiment format, used for organoid cell type annotation in SingleR
Protocols
MACS sorting NPCs
Detailed protocol from our 2019 paper . Sorting neural progenitor cultures to deplete CD271 positive cells and enrich for CD133 positive cells results in fewer infiltrating glia in directly differentiated neuronal cultures, and more consistency in differentiations between cell lines.
If you use this protocol in your work, please cite this paper
Astrocyte differentiation
Detailed protocol from our 2017 paper . Easy and efficient method of generating astrocytes from NPC cultures within 30 days
If you use this protocol in your work, please cite this paper
General iPSC to neuron directed differentiation protocol
If you use this protocol in your work, please cite this paper