Maturation and circuit integration of transplanted human cortical organoids

Repository for code used to analyze single-nuclei RNA sequencing data from transplanted human brain cortical organoids (t-hCO; also known as spheroids or t-hCS) for accompanying paper:

Revah R^*, Gore F^*, Kelley KW^*, Andersen J, Sakai N, Chen X, Li MY, Birey F, Yang X, Saw NL, Baker SW, Amin ND, Kulkarni S, Mudipalli R, Cui B, Nishino S, Grant GA, Knowles JK, Shamloo M, Huguenard JR, Deisseroth K, Pașca SP. Maturation and circuit-level integration of transplanted human cortical organoids. Nature (2022)

Nature: https://www.nature.com/articles/s41586-022-05277-w

Data links

Raw and processed data available through GEO: GSE190815

GEO_ID	Condition	Diff. days	Line
GSM5732392	t-hCO (aka t-hCS)	276	8119-1
GSM5732393	t-hCO (aka t-hCS)	224	2242-1
GSM6225773	t-hCO (aka t-hCS)	227	2242-1
GSM5732394	hCO (aka hCS)	243	1208-2
GSM6225774	hCO (aka hCS)	257	8119-1
GSM6225775	hCO (aka hCS)	227	2242-1

Processed and integrated Seurat binarized R objects in .rds format:

• transplanted hCS .rds file 2GB
• hCS .rds file 2GB

Preprocessing

Combined human and rat genome references were created usng 10x Cellranger software suite. Reference notes can be found here: Combined_HumanRat_reference.sh

Count matrices were created using Cellranger count v6.1.2 and processed on the 10x cloud analysis server. Following paramters were used:include_introns: true

To identify putative high-quality human nuclei from transplanted cortical organoids the following processing code was used: Preprocess.R

Analysis scrips

Code to generate QC plots from Extended Data Figure 4: QC_plots.R

Code to generate t-hCS plots in Figure 1 and Extended Data Figure 4: t-hCS_plots.R

Code to generate hCS plots in Extended Data Figure 4: hCS_plots.R

Code to perform pseudobulk differential expression analysis using Libra package for Supplementary Table 5: GluN_DE_analysis.R

Code to perform gene set significance testing and heatmap plots from activity-dependent gene sets displayed in Figure 2: ActivityGenePlots.R

Code to generate psychENCODE/BrainSpan plots as shown in Extended Data Figure 5: psychENCODE_plots.R

Code to perform cluster overlap mapping to reference datasets as shown in Extended Data Figure 5: Dataset_clusterMapping.R

Code to perfrom glutamatergic neuron transfer labeling from adult Allen brain references as shown in Extended Data Figure 5: GluN_Allen_mapping.R

Example outputs from above code: output