Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes

. Author manuscript; available in PMC: 2024 May 1.

Published in final edited form as: Cell. 2024 Mar 18;187(8):1955–1970.e23. doi: 10.1016/j.cell.2024.02.025

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-SOX10 Alexa Fluor 647	Novus Biologicals	Clone SOX10/991; catalog number: NBP2-59621
Mouse monoclonal anti-NeuN Alexa Fluor 488	Millipore	Clone A60; catalog number MAB377; RRID: AB_2149209
Mouse monoclonal anti-Connexin 43/GJA1 Alexa Fluor 647	Novus Biologicals	Clone 578618; catalog number FAB7737R
Rabbit monoclonal anti-SOX9 Alexa Fluor 488	Abcam	Clone EPR14335; catalog number ab196450; RRID: AB_2665383
Mouse monoclonal anti-Glial Fibrillary Acidic Protein Alexa Fluor 647	Millipore	Clone GA5; catalog number MAB3402; RRID: AB_94844
Biological samples
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB1278
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5817
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5871
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB4638
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB1465
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5559
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB4643
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5087
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB936
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5451
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5666
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5943
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5572
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5219
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5171
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5657
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB5823
Post-mortem fresh-frozen human brain prefrontal cortex tissue	NIH Neurobiobank at the University of Maryland Brain and Tissue Bank	UMB4976
Post-mortem fresh-frozen human brain prefrontal cortex tissue	Boston University UNITE or VA-BU-CLF Brain Bank	301159
Post-mortem fresh-frozen human brain prefrontal cortex tissue	Boston University UNITE or VA-BU-CLF Brain Bank	190106
Critical commercial assays
ResolveDNA Whole Genome Amplification Kit (Formerly SkrybAmpTM EA WGA Kit)	BioSkryb Genomics	P00001 - 07292022
KAPA HyperPlus Kit	Roche	Kit code KK8514; catalog number 07962428001
PicoGreen binding Quant-iT dsDNA Assay Kit	Thermo Fisher Scientific	Catalog number P7589
SeqCap Adapter Kit	Roche	Catalog number 07141548001
TapeStation HS DS100 Screen Tape	Agilent	Catalog number PN 5067-5584
REPLI-g Single Cell Kit	Qiagen	Catalog number 150345
Truseq DNA PCR-free (350bp insert)	Illumina
Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kits v3.1	10X Genomics	Catalog numbers PN-1000121 and PN-1000128
Chromium Next GEM Chip G Single Cell Kits	10X Genomics	Catalog numbers PN-1000120 and PN-1000127
Single Index Kit T Set A, 96 rxns	10X Genomics	Catalog number PN-1000213
Chromium Next GEM Single Cell ATAC Library & Gel Bead Kits	10X Genomics	Catalog numbers PN-1000175 and PN-1000176
Chromium Next GEM Chip H Single Cell Kits	10X Genomics	Catalog numbers PN-1000161 and PN-1000162
Chromium i7 Multiplex Kit N, Set A, 96 rxns	10X Genomics	PN-1000084
CellsDirect cDNA synthesis kit	Thermo Fisher Scientific	Catalog number: 18080200
Deposited data
Single neuron (PTA) and matched bulk whole genome sequencing data	Luquette et al.¹⁰	[dbGaP]: [phs001485.v3.p1]
Single nucleus RNA-seq data for UMB1465	Bizzotto et al.⁸; This study	[dbGaP]: [phs001485.v2.p1]; [NIAGADS]: [NG00162]
Single nucleus ATAC-seq data for UMB1465	Bizotto et al.⁸	[dbGaP]: [phs001485.v2.p1]
Single oligodendrocyte whole genome sequencing data	This study	[NIAGADS]: [NG00162]
Single neuron and matched bulk whole genome sequencing data for samples 301159 and 190106	This study	[NIAGADS]: [NG00162]
Single nucleus ATAC-seq	This study	[NIAGADS]: [NG00162]
Single nucleus RNA-seq for UMB4638 and UMB4643	This study	[NIAGADS]: [NG00162]
Oligonucleotides
GAPDH VIC-MGB 2X TaqMan probe	Thermo Fisher Scientific	Assay ID: Hs02786624_g1; catalog number: 4448490
ACTB VIC-MGB 2X TaqMan probe	Thermo Fisher Scientific	Assay ID: Hs01060665_g1; catalog number: 4448490
CSPG4 FAM-MGB 2X TaqMan probe	Thermo Fisher Scientific	Assay ID: Hs00361541_g1; catalog number: 4351370
PDGFR1 VIC-MGB 2X TaqMan probe	Thermo Fisher Scientific	Assay ID: Hs00998018_m1; catalog number: 4448490
MBP VIC-MGB 2X TaqMan probe	Thermo Fisher Scientific	Assay ID: Hs00921945_m1; catalog number: 4448490
PLP1 FAM-MGB 2X TaqMan probe	Thermo Fisher Scientific	Assay ID: Hs01555268_m1; catalog number: 4351370
Software and algorithms
cellranger 6.0.0	10x Genomics	https://www.10xgenomics.com/support/software/cell-ranger/latest
Seurat 3.9.9.9010	Stuart et al.⁶³	https://satijalab.org/seurat/
cellranger-atac 1.1.0	10x Genomics	https://support.10xgenomics.com/single-cell-atac/software/overview/welcome
Signac 1.1.0	Stuart et al.⁶⁴	https://stuartlab.org/signac/
bwa 0.7.17-r1188		https://github.com/lh3/bwa
SCAN2 1.1	Luquette et al.¹⁰	https://github.com/parklab/SCAN2
GATK 4.0.3.0	Broad Institute	https://gatk.broadinstitute.org
sentieon driver v202112.06	Sentieon, Inc	https://www.sentieon.com
SigProfilerExtractor 1.1.21	Islam et al.⁴⁸	https://github.com/AlexandrovLab/SigProfilerExtractor
SigProfilerMatrixGenerator 1.2.17	Bergstrom et al.⁶⁵	https://github.com/AlexandrovLab/SigProfilerMatrixGenerator
bedGraphToBigWig 2.9	UCSC Genome Browser	http://hgdownload.soe.ucsc.edu/admin/exe/
bigWigAverageOverBed 2	UCSC Genome Browser	http://hgdownload.soe.ucsc.edu/admin/exe/
lme4 1.1_33 (R package)	CRAN	https://github.com/lme4/lme4/
lmerTest 3.1_33 (R package)	CRAN	https://github.com/runehaubo/lmerTestR
Custom scripts for figures and analysis v2.0	This study; Zenodo	https://doi.org/10.5281/zenodo.10784220
SnpEff 4.3t	Cingolani⁴⁴	http://pcingola.github.io/SnpEff/
rtracklayer 1.54.0 (R package)	Bioconductor	https://doi.org/10.18129/B9.bioc.rtracklayer