Resource	Source/reference	Identifier/URL
Biological Samples
Frozen human anterior cingulate cortex samples	Parkinson’s UK Tissue Bank
Critical Commercial Assays
Chromium Single Cell 3’ Gene Expression Kit, v2	10 × Genomics	PN-120237
Qubit dsDNA HS Assay Kit	ThermoFisher	Q32851
Bioanalyzer High-Sensitivity DNA Kit	Agilent	5067-4627
QIAzol	Qiagen	79306
RNeasy 96 Kit	Qiagen	74181
TruSeq Stranded mRNA Library Prep Kit	Illumina	20020594
xGen UDI-UMI Adapters, 1–96	Integrated DNA Technologies	10005903
Deposited Data
ATtRACT database (v 0.99β)	Giudice et al., 2016 [45]	https://attract.cnic.es/index
Cell-type marker genes	Wang et al., 2018	http://resource.psychencode.org/ (DER-21_Single_cell_markergenes_UMI.xlsx)
ENCODE blacklist regions (v 2)	Amemiya et al., 2019 [7]	https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz
Ensembl GRCh38 Ensembl v97	Ensembl genome browser	ftp://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz
H-MAGMA: Hi-C gene-SNP pairs for adult dorsolateral prefrontal cortex	Sey et al., 2020 [96]	https://github.com/thewonlab/H-MAGMA/blob/master/Input_Files/Adult_brain.genes.annot
Gencode v26		https://www.gencodegenes.org/human/release_26lift37.html
GTEx portal (v 8)	GTEx Consortium, 2015 [46]	https://www.gtexportal.org/
LDSC baseline annotations (v 1.2)	Finucane et al., 2015 [41]	https://data.broadinstitute.org/alkesgroup/LDSCORE/
PD-associated genes	Blauwendraat et al., 2020 [16]
PD-associated pathways	Bandres-Ciga et al., 2020 [12]	https://pdgenetics.shinyapps.io/pathwaysbrowser/
Recount2	Collado-Torres et al., 2015 [32]	https://jhubiostatistics.shinyapps.io/recount/
Software and Algorithms
Analysis of Motif Enrichment (AME, v 5.1.1)	McLeay et al., 2010 [75]	http://meme-suite.org/doc/ame.html?man_type=web
Bulk-tissue RNA-sequencing pipeline		https://github.com/RHReynolds/RNAseqProcessing
Cell Ranger (v 3.0.2)	10 × Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation
clusterProfiler (v 3.14.3)	Yu et al., 2012 [115]	https://github.com/YuLab-SMU/clusterProfiler
Conos (v 1.1.2)	Barkas et al., 2019 [13]	https://github.com/kharchenkolab/conos
ComplexHeatmap (v 2.7.7)	Gu et al., 2016 [47]	https://github.com/jokergoo/ComplexHeatmap
DESeq2 (v 1.26.0)	Love et al., 2014 [68]	https://github.com/mikelove/DESeq2
Detecting Aberrant Splicing Events from RNA-sequencing (dasper, v 1.1.4)	Zhang et al., 2021 [117]	https://github.com/dzhang32/dasper
DoubletFinder (v 2.0.2)	McGinnis et al., 2019 [72]	https://github.com/chris-mcginnis-ucsf/DoubletFinder
DropletUtils (v 1.6.1)	Lun et al., 2019 [69]	https://github.com/MarioniLab/DropletUtils
EWCE (v 0.99.2)	Skene et al., 2016 [98]	https://github.com/NathanSkene/EWCE
Factoextra (v 1.0.7)		https://github.com/kassambara/factoextra
Fastp (v 0.20.0)	Chen et al., 2018 [28]	https://github.com/OpenGene/fastp
FastQC (v 0.11.8)	Andrews et al., 2010 [8]	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
GoSemSim (v 2.17.0)	Yu et al., 2010 [114]	https://github.com/YuLab-SMU/GOSemSim
ggplot2 (v 3.3.2)		https://ggplot2.tidyverse.org/
LDSC (v 1.0.1)	Bulik-Sullivan et al., 2015 [23]	https://github.com/bulik/ldsc
Leafcutter (v 0.2.8)	Li et al., 2018 [65]	https://github.com/davidaknowles/leafcutter/
Limma (v 3.42.2)	Ritchie et al., 2015 [91]	https://github.com/cran/limma
MAGMA (v 1.0.8b)	de Leeuw et al., 2015 [63]	https://ctg.cncr.nl/software/magma
MashMap2 (v 2.0)	Jain et al., 2018 [53]	https://github.com/marbl/MashMap
MAST (v 1.12.0)	Finak et al., 2015 [40]	https://github.com/RGLab/MAST/
recount (v 1.11.8)	Collado-Torres et al., 2015 [32]	https://github.com/leekgroup/recount
rrvgo (v 1.1.4)	Sayols et al., 2020 [94]	https://ssayols.github.io/rrvgo/
RSeQC (v 2.6.4)	Wang et al., 2012 [111]	http://rseqc.sourceforge.net/
rtracklayer (v 1.46.0)	Lawrence et al., 2009 [62]	https://github.com/lawremi/rtracklayer
rutils (v 0.99.2)		https://github.com/RHReynolds/rutils
Salmon (v 0.14.1)	Patro et al., 2017 [86]	https://salmon.readthedocs.io/en/latest/index.html
Seurat (v 3.2.0)	Stuart et al. 2019 [103]	https://github.com/satijalab/seurat/
Scaden (v 0.9.2)	Menden et al., 2020 [76]	https://github.com/KevinMenden/scaden
STAR (v 2.7.0a)	Dobin et al., 2013 [35]	https://github.com/alexdobin/STAR
Tximport (v 1.14.2)	Soneson et al., 2015 [101]	https://github.com/mikelove/tximport
UMAP (v 0.1.10)	McInnes et al., 2018 [73]	https://github.com/lmcinnes/umap
WebGestaltR (v 0.4.4)	Liao et al. [67]	https://github.com/bzhanglab/WebGestaltR