Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements

. 2023 Feb 2;3(3):100263. doi: 10.1016/j.xgen.2023.100263

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Rabbit anti-ZEB1 antibody	Bethyl	Cat#: A301-921A; RRID: AB_1524109
Rabbit polyclonal MEF2C antibody	proteintech	Cat#: 18290-1-AP; RRID: AB_2142849
Dynabeads™ M−280 Sheep Anti-Rabbit IgG	ThermoFisher Scientific	Cat#: 11203D; RRID: AB_2783009
Anti-NeuN Antibody, clone A60, Alexa Fluor®488 conjugated	Millipore Sigma	Cat#: MAB377X; RRID: AB_2149209
Recombinant Anti-Olig2 antibody [EPR2673]	Abcam	Cat#: ab109186; RRID: AB_10861310

Biological samples

Human brain tissue	NIH NeuroBioBank	https://neurobiobank.nih.gov
Human brain tissue	Pritzker Neuropsychiatric Disorders Research Consortium	https://pritzkerneuropsych.org/www/about-us/scientific-approach/brain-bank

Chemicals, peptides, and recombinant proteins

SPRI Select Reagent	Fisher Scientific	Cat#: NC0406407
Lipofectamine LTX with Plus Reagent	ThermoFisher Scientific	Cat#: 15338100
Protector RNAse inhibitor	Millipore Sigma	Cat#: 3335399001
Poly-L-ornithine solution	Millipore Sigma	Cat#: P4957-50ML
UltraPure 1M Tris-HCl, pH 8.0	Fisher Scientific	Cat#: 15568-025
Calcium Chloride Solution	Millipore Sigma	Cat#: 21115-100ML
Magnesium Acetate Solution	Millipore Sigma	Cat#: 63052-100ML
DTT, 1M	ThermoFisher Scientific	Cat#: P2325
EDTA, 0.5M	Millipore Sigma	Cat#: 324506-100ML
Triton X-100	Millipore Sigma	Cat#: T8787-100ML
OmniPur Sucrose	Millipore Sigma	Cat#: 8510-500GM
Bovine Serum Albumin Fraction V, protease-free	Millipore Sigma	Cat#: 3117332001
Tween 20	Millipore Sigma	Cat#: P9416-50ML
NP-40	Fisher Scientific	Cat#: 28324
Digitonin (5%)	ThermoFisher Scientific	Cat#: BN2006
PMSF	Millipore Sigma	Cat#: 10837091001
cOmplete protease inhibitor cocktail	Millipore Sigma	Cat#: 11697498001
Corning® 10X Phosphate-Buffered Saline (PBS), pH 7.4 ± 0.1, Liquid without calcium and magnesium, RNase-/DNase- and protease-free	Corning	Cat#: 46-013-CM
Sodium Deoxycholate 10%	BioWorld	Cat#: 40430018-2
UltraPure SDS Solution, 10%	ThermoFisher Scientific	Cat#: 15553027
Pierce™ 16% Formaldehyde (w/v), Methanol-free	ThermoFisher Scientific	Cat#: 28906
BioUltra Glycine	Millipore Sigma	Cat#: 50046-250G
DAPI Solution (1 mg/mL)	ThermoFisher Scientific	Cat#: 62248
Lithium chloride solution	Millipore Sigma	Cat#: L7026-500ML
Sodium Bicarbonate	Millipore Sigma	Cat#: S5761-500G
Proteinase K	Lucigen	Cat#: MPRK092
RNase A	Qiagen	Cat#: 19101

Critical commercial assays

Nano-Glo Dual-Luciferase Reporter Assay System	Promega	Cat#: N1630
Global Diversity Array + NeuroBooster	Illumina	Cat#: 20031816
Chromium Next GEM Chip J	10X Genomics	Cat#: PN-1000230
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle	10X Genomics	Cat#: PN-1000283
Dual Index Kit TT Set A	10X Genomics	Cat#: PN-1000215
DNeasy Blood and Tissue Kit	Qiagen	Cat#: 69506
Qubit dsDNA HS Assay Kit	ThermoFisher Scientific	Cat#: Q32854
Standard Sensitivity NGS Fragment Analysis Kit	Advanced Analytical	Cat#: DNF-473

Deposited data

Raw and analyzed data	This paper	GEO: GSE214637
Code	https://doi.org/10.5281/zenodo.7405971	https://github.com/aanderson54/scMultiomics_AD

Experimental models: Cell lines

HEK293	ATCC	Cat# CRL-1573, RRID:CVCL_0045
293FT	ThermoFisher Scientific	Cat#: R70007, RRID:CVCL_6911

Recombinant DNA

pGL4.23 [luc2/minP]	Promega	Cat#: E8411
pNL1.1.CMV[Nluc/CMV]	Promega	Cat#: N1091

Software and algorithms

Prism v9	Graph Pad	https://www.graphpad.com/scientific-software/prism/
BioConductor v1.30.16	Huber et al.⁹³	https://www.bioconductor.org
scDblFinder v1.9.4	Germain et al.⁹⁴	https://github.com/plger/scDblFinder
Seurat v4.1.1	Hao et al.²²	https://github.com/satijalab/seurat
sctransform v0.3.3	Hafemeister and Satija⁹⁵	https://github.com/satijalab/sctransform
Harmony v0.1.0	Korsunsky et al.⁹⁶	https://github.com/immunogenomics/harmony
MAST v1.20.0	Finak et al.⁹⁷	https://github.com/RGLab/MAST
R v4.1.1	CRAN	https://cran.r-project.org
enrichR v3.0.0	Chen et al.⁹⁸	https://github.com/wjawaid/enrichR
MACS2 v2.2.71	Zhang et al.⁹⁹	https://github.com/macs3-project/MACS
Signac v1.6.0	Stuart et al.²³	https://github.com/stuart-lab/signac
ComplexHeatmap v2.10.0	Gu et al.¹⁰⁰	https://github.com/jokergoo/ComplexHeatmap
GenomicRanges v1.46.1	Lawrence et al.¹⁰¹	https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
rtracklayer v1.54.0	Lawrence et al.¹⁰²	https://bioconductor.org/packages/release/bioc/html/rtracklayer.html
ChIPseeker v1.30.3	Yu et al.¹⁰³	https://github.com/YuLab-SMU/ChIPseeker
cellSNP 1.2.2	Huang and Huang¹⁰⁴	https://github.com/hxj5/cellsnp-lite
vireo v0.5.6	Huang et al.¹⁰⁵	https://github.com/single-cell-genetics/vireo
sLDSC v1.0.1	Finucane et al.⁵⁴	https://github.com/bulik/ldsc
ENCODE ChIP-seq pipeline2	ENCODE DCC	https://github.com/ENCODE-DCC/chip-seq-pipeline2
CellRanger arc 2.0.1	10X Genomics	http://software.10xgenomics.com