KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Experimental Models: Animals | ||
| Mouse: C57BL/6J | Jackson Labs | Cat# 664; RRID:IMSR_JAX:000664 |
| Chemicals, peptides, and recombinant proteins | ||
| Formamide | Ambion | Cat# AM9342 |
| 20xSSC | Ambion | Cat# AM9763 |
| Triton X- | Sigma | Cat# T8787 |
| Glucose oxidase | Sigma | Cat# G2133 |
| Phusion® Hot Start Flex 2X Master Mix | New England Biolabs | Cat# M0536 |
| Maxima H Minus Reverse Transcriptase | ThermoFisher | Cat# EP0752 |
| dNTP mix | ThermoFisher | Cat# R1121 |
| 32% Paraformaldehyde | Electron Microscopy Sciences | Cat# 15714S |
| RNase inhibitor, Murine | New England Biolabs | Cat# M0314 |
| 1M Tris, pH 8 | ThermoFisher | Cat# 15568025 |
| Catalase | Sigma | Cat# C3155 |
| 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox) | Sigma | Cat# 238813 |
| Tris(2-carboxyethyl)phosphine (TCEP) HCl | GoldBio | Cat# TCEP1 |
| Hoescht 33,342, Trihydrochloride, Trihydrate | ThermoFisher | Cat# H3570 |
| Lipopolysaccharides from E. coli O 111:B4 | Sigma | Cat# L4391 |
| Yeast tRNA | ThermoFisher | Cat# AM7119 |
| Dextran sulfate | Sigma | Cat# S4030 |
| Ethanol | Decon Labs | Cat# V1016 |
| SDS | ThermoFisher | Cat# 15553027 |
| Proteinase K | New England Biolabs | Cat# P8107S |
| Ethylene carbonate | Sigma | Cat# 676802–1L |
| Glucose | Sigma | Cat# G7021 |
| Oligonucleotides | ||
| Readout probes | Integrated DNA Technologies | See Table S3 |
| Encoding oligonucleotide probe library | Twist Biosciences | See Table S2 |
| Anchor probe:/5Acryd/TTGAGTGGATGGAGTGTAATT+TT+TT + TT + TT + TT + TT + TT + TT + TT + T | Integrated DNA Technologies | N/A |
| Software and algorithms | ||
| Custom analysis software | This paper | https://github.com/ZhuangLab/SpatialBrainAgingCell22 |
| MERlin | Xia et al.62 | https://github.com/ZhuangLab/MERlin |
| Scrublet | Wolock et al.63 | https://github.com/swolock/scrublet |
| Anndata | Virshup et al.64 | https://github.com/scverse/anndata |
| BBKNN | Polahski et al.65 | https://github.com/Teichlab/bbknn |
| Harmony | Korsunsky et al.35 | https://github.com/slowkow/harmonypy |
| Scanpy | Wolf et al.66 | https://github.com/scverse/scanpy |
| Allcools | Liu et al.38 | https://github.com/lhqing/ALLCools |
| Cellpose | Stringer et al.67 | https://github.com/MouseLand/cellpose |
| Deposited data | ||
| snRNA-seq data | This paper | GEO: GSE207848 |
| snRNA-seq data and MERFISH data | This paper | https://cellxgene.cziscience.com/collections/31937775-0602-4e52-a799-b6acdd2bac2e |