Table 1:

Single-cell or Single-nucleus RNA sequencing studies on human post-mortem brain tissue in people with neurobiological disorders.

Study	Condition Studied	N	Brain Regions; Cell Types; Number of Nuclei/Cells Analyzed	Platform	Main Findings
Pfisterer et al. (2020)	Epilepsy	10 controls, 9 temporal lobe epilepsy samples	Temporal cortex; Neurons; 101,982 cells	10× Genomics; Smart-seq2	Genes involved in hyperexcitability, such as glutamate receptors, neurotransmitter synthesis genes, etc. were altered in epilepsy neurons
Kumar et al. (2022)	Epilepsy	Number of control samples not specified, 6 epilepsy samples	Olfactory, frontal, and temporal lobes; Immune cells; 85,780 cells	10× Genomics	Increased pro-inflammatory gene expression in microglia; Infiltration of activated, cytotoxic leukocytes
Jäkel et al. (2019)	Multiple sclerosis	5 controls, 4 MS samples	White matter (brain region not specified); All cell types; 17,799 cells	10× Genomics	Altered oligodendrocyte subclusters and upregulation of myelin-related genes in MS oligodendrocytes
Grubman et al. (2019)	Alzheimer’s	6 controls, 6 AD samples	Entorhinal cortex; All cell types; 13,214 cells	10× Genomics	Upregulation of stress response genes in all cell types; downregulated synapse-associated genes in neurons; increased immune gene expression in microglia, astrocytes, and endothelial cells; identification of cell-specific AD gene regulatory networks
Mathys et al., 2019	Alzheimer’s	24 controls, 24 AD samples	Prefrontal cortex (Brodmann area 10); All cell types; 80,660 cells	10× Genomics	Altered myelination-related gene expression in multiple cell types; Upregulation of microglial and astrocyte activation genes; Increased global stress response gene expression in all cell types in late-stage AD
Zhou et al. (2020)	Alzheimer’s	11 controls, 11 AD with TREM2-common variant, 10 AD with TREM2-R62H; 5 AD with TREM2-R47H and 5 AD with TREM2-common variant	Dorsolateral prefrontal cortex/parietal cortex; All cell types; 73,419 cells	10× Genomics	Decreased expression of microglial activation genes in TREM2-R62H and R47H microglia compared to TREM2 common variant microglia in AD
Leng et al. (2021)	Alzheimer’s	10 samples: 3 Braak stage 0, 4 Braak stage 2, 3 Braak stage 6	Entorhinal cortex/ superior frontal gyrus; All cell types; 42,528 cells from EC and 63,608 cells from SFG	10× Genomics	Reduced numbers of excitatory neurons in late-stage AD; increased microglial numbers
Belonwu et al. (2022a)	Alzheimer’s	30 controls, 30 AD samples	Prefrontal cortex/ entorhinal cortex; All cell types; 70,634 cells from PFC and 13,214 cells from EC	10× Genomics	Differential cell-specific gene expression in AD based on APOE genotype
Belonwu et al. (2022b)	Alzheimer’s	27 controls, 26 AD samples	Prefrontal cortex/ entorhinal cortex; All cell types; 70,634 cells from PFC and 13,214 cells from EC	10× Genomics	Differential cell-specific gene expression in AD based on sex
Velmeshev et al. (2019)	Autism	16 controls, 15 ASD samples	Prefrontal cortex, anterior cingulate cortex; All cell types; 104,559 cells	10× Genomics	Differential expression of genes involved in synaptic function and brain development in ASD neurons; differential expression of activation genes in ASD microglia
Brenner et al. (2020)	Alcohol dependence	4 controls, 3 alcohol dependence samples	Prefrontal cortex; All cell types; 16,305 cells	10× Genomics	Glial cells showed the most differentially expressed genes, including neuroinflammation genes
Nagy et al. (2020)	Major Depressive Disorder	17 controls, 17 MDD samples	Dorsolateral prefrontal cortex; all cell types; 78,886 cells	10× Genomics	Oligodendrocyte precursor cells and deep excitatory neurons showed the most differentially expressed genes; genes involved in synaptic plasticity, cell signaling, the innate immune system, and cytoskeletal function were most dysregulated

Study	Quality Control	Data Availability
Pfisterer et al. (2020)	• Cells with >8% mitochondrial genes removed • Doublet cells removed	European Genome-phenome Archive (EGA): EGAS00001002882.
Kumar et al. (2022)	• Cells with <300 genes or > 5000 genes removed • Cells with >20% mitochondrial genes removed	Gene Expression Omnibus (GEO): GSE201048 Additional: Raw counts and analyzed R objects are also available at https://epicimmuneatlas.org/NatNeu2022. Associated data used to produce figures are also deposited in the Zenodo repository (https://doi.org/10.5281/zenodo.6477100).
Jäkel et al. (2019)	• Cells with <200 genes removed • Cells with >20% mitochondrial genes removed	European Genome-phenome Archive (EGA): EGAS00001003412. Gene Expression Omnibus (GEO): GSE118257. Additional: A browsable web resource is available at https://ki.se/en/mbb/oligointernode.
Grubman et al. (2019)	• Cells outside 5th and 95th percentile with respect to number of total and unique genes were removed • Cells with >10% mitochondrial genes removed	Gene Expression Omnibus (GEO): GSE138852. Additional: Data can also be visualized via the interactive web application at adsn.ddnetbio.com. Single-cell gene expression data and metadata can also be downloaded directly via adsn.ddnetbio.com.
Mathys et al., 2019	• Cells with <200 genes removed • Cells with abnormally high ratio of mitochondrial genes removed	The Rush Alzheimer’s Disease Center (RADC) Research Resource Sharing Hub: https://www.radc.rush.edu/docs/omics.htm (snRNA-seq PFC) Synapse: (https://www.synapse.org/#!Synapse:syn18485175) under the doi https://doi.org/10.7303/syn18485175. The Religious Orders Study and Memory and Aging Project (ROSMAP) metadata can be accessed at https://www.synapse.org/#!Synapse:syn3157322. The data are available under controlled use conditions set by human privacy regulations. To access the data, a data use agreement is needed.
Zhou et al. (2020)	• Cells with >5% mitochondrial genes removed • Cells with <400 genes or > 7000 genes removed	Murine data: Gene Expression Omnibus (GEO): GSE140511 Human data: AD Knowledge Portal (https://adknowledgeportal.org) under study snRNAseqAD_TREM2 and are also accessible through Synapse at https://doi.org/10.7303/syn21125841. Additional ROSMAP data can be requested at https://www.radc.rush.edu/.
Leng et al. (2021)	• Cells with <200 unique genes excluded	Gene Expression Omnibus (GEO): GSE147528. Additional: Processed data is available at Synapse.org under the Synapse ID syn21788402 and can also be explored interactively through the CellXGene platform at https://kampmannlab.ucsf.edu/ad-brain. Data from Mathys et al. (above) was also used in this study.
Belonwu et al. (2022a)	• Cells outside 5th and 95th percentile with respect to number of total and unique genes were removed • Cells with >10% mitochondrial genes removed	The authors utilized previously publicly available datasets in this study. Prefrontal cortex from the Accelerating Medicines Partnership Alzheimer’s Disease Project (AMP-AD) Knowledge Portal under the Religious Orders Study and Memory and Aging Project (ROSMAP) (https://www.synapse.org/#!Synapse:syn18485175 and https://www.synapse.org/#!Synapse:syn3157322). Entorhinal cortex from a data repository provided by Grubman et al. (2019) (http://adsn.ddnetbio.com/). Data from the entorhinal cortex may also be accessed from the Gene Expression Omnibus under the accession number GSE138852. Access to the prefrontal cortex dataset requires a formal request to ROSMAP.
Belonwu et al. (2022b)	• Cells outside 5th and 95th percentile with respect to number of total and unique genes were removed • Cells with >10% mitochondrial genes removed	See above.
Velmeshev et al. (2019)	• Cells with unique number of genes <500 removed • Cells with >5% mitochondrial genes removed	Sequence Read Archive (SRA): PRJNA434002. Additional: Analyzed data and visualization are available at https://autism.cells.ucsc.edu.
Brenner et al. (2020)	• >20% mitochondrial genes removed	Gene Expression Omnibus (GEO): GSE141552.
Nagy et al. (2020)	• Cells with fewer than 110 genes removed • Cells with top 0.5% number of genes removed • Other custom filtering	Gene Expression Omnibus (GEO): GSE144136.