Recombinant:Article Title: Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alexa Fluor 488–conjugated anti-NeuN antibody Millipore Cat# MAB377X; Clone A60; RRID: AB_2149209 Chemicals, peptides, and recombinant proteins Hoechst 33342 Thermo Fisher Scientific Cat# 62249 Proteinase K Zymo Cat# D3001-2-20 CT Conversion Reagent Zymo Cat# D5003-1 M-Digestion Buffer Zymo Cat# D5021-9 Adaptase kits IDT Cat# 10010130 Custom 3C Kits for single cell (8 reactions) Arima Genomics N/A Sample Preparation Kit Vizgen Cat# 10400012 MERSCOPE 500 Gene Imaging Kit Vizgen Cat# 10400006 Critical commercial assays MERFISH Data Generation Vizgen https://vizgen.com/wp-content/uploads/ 2025/04/91600129_Histology-Guide-forPreparing-Fresh-and-Fixed-FrozenTissue-Samples_Rev-B.pdf snmC-seq3 and snm3C-seq Protocol This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1 Deposited data Male single-cell FASTQ (2-month) Liu et al. 36 GEO: GSE132489; GEO: GSE213262 Male single-cell FASTQ This Paper GEO: GSE313770 Female single-cell FASTQ This Paper GEO: GSE292803 Female single-cell Contact This Paper GEO: GSE292803 Male Cell type pseudo-bulk AllC This Paper GEO: GSE313770 Female Cell type pseudo-bulk AllC This Paper GEO: GSE292803 snATAC-seq Amaral et al. 30 GEO: GSE294772 10X Multiome Amaral etal. .. 30 GEO: GSE294772 H3K9me3 bigwig Zhang et al. 28 GEO: GSE187332 CTCF ChIP-seq ENCODE 73 ENCODE: ENCSR677HXC Experimental models: Organisms/strains C57BL/6J Jackson Laboratory 000664 Oligonucleotides Random primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials PCR i5 primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials PCR i7 primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials Software and algorithms Custom analysis software This paper https://github.com/rachelzeng98/ aging-mouse-brain.git EpiAgingTransformer Model This paper https://github.com/Michaelvll/ aging-gene-prediction Full Software Versions This Paper See Table S9 (Continued on next page) ll OPEN ACCESS e1 Cell 189, 1–19.e1–e9, April 2, 2026 Please cite this article in press as: Zeng et al., Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain, Cell (2026), https://doi.org/10.1016/j.cell.2026.02.015 Resource
Single Cell:Article Title: Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alexa Fluor 488–conjugated anti-NeuN antibody Millipore Cat# MAB377X; Clone A60; RRID: AB_2149209 Chemicals, peptides, and recombinant proteins Hoechst 33342 Thermo Fisher Scientific Cat# 62249 Proteinase K Zymo Cat# D3001-2-20 CT Conversion Reagent Zymo Cat# D5003-1 M-Digestion Buffer Zymo Cat# D5021-9 Adaptase kits IDT Cat# 10010130 Custom 3C Kits for single cell (8 reactions) Arima Genomics N/A Sample Preparation Kit Vizgen Cat# 10400012 MERSCOPE 500 Gene Imaging Kit Vizgen Cat# 10400006 Critical commercial assays MERFISH Data Generation Vizgen https://vizgen.com/wp-content/uploads/ 2025/04/91600129_Histology-Guide-forPreparing-Fresh-and-Fixed-FrozenTissue-Samples_Rev-B.pdf snmC-seq3 and snm3C-seq Protocol This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1 Deposited data Male single-cell FASTQ (2-month) Liu et al. 36 GEO: GSE132489; GEO: GSE213262 Male single-cell FASTQ This Paper GEO: GSE313770 Female single-cell FASTQ This Paper GEO: GSE292803 Female single-cell Contact This Paper GEO: GSE292803 Male Cell type pseudo-bulk AllC This Paper GEO: GSE313770 Female Cell type pseudo-bulk AllC This Paper GEO: GSE292803 snATAC-seq Amaral et al. 30 GEO: GSE294772 10X Multiome Amaral etal. .. 30 GEO: GSE294772 H3K9me3 bigwig Zhang et al. 28 GEO: GSE187332 CTCF ChIP-seq ENCODE 73 ENCODE: ENCSR677HXC Experimental models: Organisms/strains C57BL/6J Jackson Laboratory 000664 Oligonucleotides Random primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials PCR i5 primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials PCR i7 primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials Software and algorithms Custom analysis software This paper https://github.com/rachelzeng98/ aging-mouse-brain.git EpiAgingTransformer Model This paper https://github.com/Michaelvll/ aging-gene-prediction Full Software Versions This Paper See Table S9 (Continued on next page) ll OPEN ACCESS e1 Cell 189, 1–19.e1–e9, April 2, 2026 Please cite this article in press as: Zeng et al., Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain, Cell (2026), https://doi.org/10.1016/j.cell.2026.02.015 Resource
Sample Prep:Article Title: Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alexa Fluor 488–conjugated anti-NeuN antibody Millipore Cat# MAB377X; Clone A60; RRID: AB_2149209 Chemicals, peptides, and recombinant proteins Hoechst 33342 Thermo Fisher Scientific Cat# 62249 Proteinase K Zymo Cat# D3001-2-20 CT Conversion Reagent Zymo Cat# D5003-1 M-Digestion Buffer Zymo Cat# D5021-9 Adaptase kits IDT Cat# 10010130 Custom 3C Kits for single cell (8 reactions) Arima Genomics N/A Sample Preparation Kit Vizgen Cat# 10400012 MERSCOPE 500 Gene Imaging Kit Vizgen Cat# 10400006 Critical commercial assays MERFISH Data Generation Vizgen https://vizgen.com/wp-content/uploads/ 2025/04/91600129_Histology-Guide-forPreparing-Fresh-and-Fixed-FrozenTissue-Samples_Rev-B.pdf snmC-seq3 and snm3C-seq Protocol This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1 Deposited data Male single-cell FASTQ (2-month) Liu et al. 36 GEO: GSE132489; GEO: GSE213262 Male single-cell FASTQ This Paper GEO: GSE313770 Female single-cell FASTQ This Paper GEO: GSE292803 Female single-cell Contact This Paper GEO: GSE292803 Male Cell type pseudo-bulk AllC This Paper GEO: GSE313770 Female Cell type pseudo-bulk AllC This Paper GEO: GSE292803 snATAC-seq Amaral et al. 30 GEO: GSE294772 10X Multiome Amaral etal. .. 30 GEO: GSE294772 H3K9me3 bigwig Zhang et al. 28 GEO: GSE187332 CTCF ChIP-seq ENCODE 73 ENCODE: ENCSR677HXC Experimental models: Organisms/strains C57BL/6J Jackson Laboratory 000664 Oligonucleotides Random primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials PCR i5 primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials PCR i7 primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials Software and algorithms Custom analysis software This paper https://github.com/rachelzeng98/ aging-mouse-brain.git EpiAgingTransformer Model This paper https://github.com/Michaelvll/ aging-gene-prediction Full Software Versions This Paper See Table S9 (Continued on next page) ll OPEN ACCESS e1 Cell 189, 1–19.e1–e9, April 2, 2026 Please cite this article in press as: Zeng et al., Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain, Cell (2026), https://doi.org/10.1016/j.cell.2026.02.015 Resource
Imaging:Article Title: Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alexa Fluor 488–conjugated anti-NeuN antibody Millipore Cat# MAB377X; Clone A60; RRID: AB_2149209 Chemicals, peptides, and recombinant proteins Hoechst 33342 Thermo Fisher Scientific Cat# 62249 Proteinase K Zymo Cat# D3001-2-20 CT Conversion Reagent Zymo Cat# D5003-1 M-Digestion Buffer Zymo Cat# D5021-9 Adaptase kits IDT Cat# 10010130 Custom 3C Kits for single cell (8 reactions) Arima Genomics N/A Sample Preparation Kit Vizgen Cat# 10400012 MERSCOPE 500 Gene Imaging Kit Vizgen Cat# 10400006 Critical commercial assays MERFISH Data Generation Vizgen https://vizgen.com/wp-content/uploads/ 2025/04/91600129_Histology-Guide-forPreparing-Fresh-and-Fixed-FrozenTissue-Samples_Rev-B.pdf snmC-seq3 and snm3C-seq Protocol This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1 Deposited data Male single-cell FASTQ (2-month) Liu et al. 36 GEO: GSE132489; GEO: GSE213262 Male single-cell FASTQ This Paper GEO: GSE313770 Female single-cell FASTQ This Paper GEO: GSE292803 Female single-cell Contact This Paper GEO: GSE292803 Male Cell type pseudo-bulk AllC This Paper GEO: GSE313770 Female Cell type pseudo-bulk AllC This Paper GEO: GSE292803 snATAC-seq Amaral et al. 30 GEO: GSE294772 10X Multiome Amaral etal. .. 30 GEO: GSE294772 H3K9me3 bigwig Zhang et al. 28 GEO: GSE187332 CTCF ChIP-seq ENCODE 73 ENCODE: ENCSR677HXC Experimental models: Organisms/strains C57BL/6J Jackson Laboratory 000664 Oligonucleotides Random primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials PCR i5 primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials PCR i7 primer This Paper https://www.protocols.io/view/snm3c- seq3-kqdg3x6ezg25/v1/materials Software and algorithms Custom analysis software This paper https://github.com/rachelzeng98/ aging-mouse-brain.git EpiAgingTransformer Model This paper https://github.com/Michaelvll/ aging-gene-prediction Full Software Versions This Paper See Table S9 (Continued on next page) ll OPEN ACCESS e1 Cell 189, 1–19.e1–e9, April 2, 2026 Please cite this article in press as: Zeng et al., Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain, Cell (2026), https://doi.org/10.1016/j.cell.2026.02.015 Resource
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