Spatial Atlas of the Mouse Central Nervous System at Molecular Resolution
Description
Spatially charting molecular cell types at single-cell resolution across the three-dimensional (3D) volume of the brain is critical for illustrating the molecular basis of the brain anatomy and functions. Single-cell RNA sequencing (scRNA-seq) has profiled molecular cell types in the mouse brain, but cannot capture their spatial organization. Here, we employed an in situ sequencing technique, STARmap PLUS, to map 1.09 million high-quality cells across the whole adult mouse brain and the spinal cord, profiling 1,022 genes at subcellular resolution with a voxel size of 194 X 194 X 345 nm3 in 3D. We developed computational pipelines to segment, cluster, and annotate 230 molecular cell types by single-cell gene expression and 106 molecular tissue regions by spatial niche gene expression. Joint analyses of molecular cell types and molecular tissue regions enabled a systematic molecular spatial cell type nomenclature and allowed the identification of tissue architectures previously undefined in established brain anatomy. To create a transcriptome-wide spatial atlas, we further integrated the STARmap PLUS measurements with a published scRNA-seq atlas, imputing 11,844 genes at the single-cell level. Finally, we delineated the tropisms of a brain-wide transgene delivery tool, AAV-PHP.eB5,6, across the molecular cell types and tissue regions of the whole mouse brain. Together, this annotated dataset provides a comprehensive, high-resolution, single-cell resource that integrates a spatial molecular atlas, cell taxonomy, brain anatomy, and genetic manipulation accessibility of the mammalian central nervous system (CNS).
Files
cluster.csv
Files
(29.6 GB)
| Name | Size | Download all |
|---|---|---|
|
md5:abc07a41c4e1512c47748b160fa8fee1
|
125.8 MB | Preview Download |
|
md5:18d051f50915fd03125ffe70df2d5598
|
199.8 MB | Preview Download |
|
md5:b87d446114972a22111bfe7e28f2dd7b
|
12.0 MB | Preview Download |
|
md5:59ae00554187f51a1ff019a4c00427b2
|
393.8 MB | Preview Download |
|
md5:4ad7577eaeba180bf3a1eb7da4b43563
|
1.9 GB | Preview Download |
|
md5:96defe66276e3bbcf5198f29fe58cb4d
|
188.1 MB | Preview Download |
|
md5:ea4b1e7a0688a63c4a923d4d857a2c20
|
15.9 MB | Preview Download |
|
md5:7fce5c836dcaef0c37985a184c38f002
|
110.8 MB | Preview Download |
|
md5:4c4cd1082502500e6cecfd3af7bb81db
|
2.6 GB | Preview Download |
|
md5:edbdf5accc973cc0a1efbf8bb4f91425
|
255.2 MB | Preview Download |
|
md5:853f0f1f929f74f7a85323deef7eeebd
|
26.4 MB | Preview Download |
|
md5:f072fd34b186e9a7601a81d939fc4293
|
296.7 MB | Preview Download |
|
md5:4daa35f6cca94792e24c44a7f9e42a00
|
4.4 GB | Preview Download |
|
md5:77c23a872ebfec5333cd502e5cc6f198
|
428.0 MB | Preview Download |
|
md5:4477d53bcf33fba1c3bfb60d318291c9
|
127.3 MB | Preview Download |
|
md5:bfec0826a16ea81291e0f0c41380a91c
|
764.1 kB | Preview Download |
|
md5:1ddcef7e50cb066d50efea7698351fcc
|
34.7 MB | Preview Download |
|
md5:9532bc5a18191893020e23e4861b6e7b
|
122.0 MB | Preview Download |
|
md5:e1cf319401a6650f0fa0e167ab98e7bb
|
12.1 MB | Preview Download |
|
md5:a4eb6ada242c85c8f46b3865d8dae128
|
4.1 MB | Preview Download |
|
md5:61eb0f9acdd6699e4affca905b3dcc51
|
157.5 MB | Preview Download |
|
md5:45de7cc0fafd623730e920a03235a762
|
619.1 MB | Preview Download |
|
md5:f7cc15fa370ad234aa23aec422c29e83
|
61.1 MB | Preview Download |
|
md5:fffe0b28dec715b3be048f162382a769
|
1.9 MB | Preview Download |
|
md5:a750bb3bc4540e36a78bbeeb7ce4dab6
|
50.6 MB | Preview Download |
|
md5:0bf51ec9ea10fc363c9299804f35c553
|
330.7 MB | Preview Download |
|
md5:6c9841a27fe2d91bab1528ee0aada9db
|
32.5 MB | Preview Download |
|
md5:c6f013d4f608227209037fa515b874ef
|
4.8 MB | Preview Download |
|
md5:8181e3e6435391ab51890a3a3c0e5025
|
119.6 MB | Preview Download |
|
md5:20b52ca7f886ebd350885c9025c89faf
|
773.7 MB | Preview Download |
|
md5:e1043f8f792607b4ac0c71ebc5b8d949
|
76.0 MB | Preview Download |
|
md5:cab9bd0c0ff4c54bdd772a73536eec49
|
5.7 MB | Preview Download |
|
md5:7e3402195f67de0e50aeae328ff806e7
|
188.4 MB | Preview Download |
|
md5:49905ac717da83088b22ff8291ba7cae
|
930.4 MB | Preview Download |
|
md5:272fee552015334620feb2375b7d7ea8
|
91.6 MB | Preview Download |
|
md5:98efc19b7c675b95fee127c45eec179c
|
5.9 MB | Preview Download |
|
md5:8b807067486a914cafffc622a77d2ab8
|
307.6 MB | Preview Download |
|
md5:4fb0f560c40d058f59b8a90d172fdeca
|
962.7 MB | Preview Download |
|
md5:897228e1ea599177dad35b8d0d316d79
|
95.1 MB | Preview Download |
|
md5:e99d717495da86305c348b16e66fb05b
|
7.6 MB | Preview Download |
|
md5:4056c6a28db11f4d5c6915d1519ddc06
|
325.0 MB | Preview Download |
|
md5:e2918ea5417432c407a479de57111e20
|
1.2 GB | Preview Download |
|
md5:c68bcc75c6bf26840b8dfaa11f3c77da
|
119.6 MB | Preview Download |
|
md5:a7d79dcc88ad08d89762f84ba3f7b1e3
|
6.0 MB | Preview Download |
|
md5:61c8a17c9c00ffbfeb8627ff47cd136d
|
132.5 MB | Preview Download |
|
md5:ee93c2a1246550fb476911bb0a91721d
|
948.9 MB | Preview Download |
|
md5:77d225ac9de87f573626cca16eea5b19
|
93.2 MB | Preview Download |
|
md5:e47ec9eea9c5215eef175c2566eb0c87
|
6.1 MB | Preview Download |
|
md5:dacbb8b54e1bef513546e394ad447fd0
|
154.0 MB | Preview Download |
|
md5:f4853eb701af372f9c71b1d204407fe3
|
1.0 GB | Preview Download |
|
md5:1ce69036e1b5d71a21424aa4015c8bc6
|
99.4 MB | Preview Download |
|
md5:cc8bd7a887ccdb3a3a77fe1713c0ed68
|
6.0 MB | Preview Download |
|
md5:8bf4851260c417d45ba14a30644ee3ef
|
239.5 MB | Preview Download |
|
md5:801eeb5505b69492fa24d55ec9d9a8d8
|
1.1 GB | Preview Download |
|
md5:f3b80e80a1f21a5c98c807eafb1b1ae7
|
104.2 MB | Preview Download |
|
md5:3096bcf8297c66d62b1a2777d51eac39
|
4.7 MB | Preview Download |
|
md5:46116dd6edb721fb36ae9cb374eb1f64
|
109.5 MB | Preview Download |
|
md5:546ed351803ccb5c7031c0930de904e9
|
812.5 MB | Preview Download |
|
md5:383ee4b811fcd200c205ec411b3c67d8
|
79.9 MB | Preview Download |
|
md5:f4965c9e88427816c0f1bb98180a3635
|
7.5 MB | Preview Download |
|
md5:342069f3cd265f227049d208d4ae5e03
|
294.8 MB | Preview Download |
|
md5:ca3327ee770ee0f88e4ec2e84b9daa70
|
1.3 GB | Preview Download |
|
md5:319947274bb8c097fe5b0d14d52f4856
|
130.4 MB | Preview Download |
|
md5:3c9043b593b9baa7c353d63902ce232a
|
5.6 MB | Preview Download |
|
md5:9bb9afd68f96782e5512d3b470971ecc
|
290.4 MB | Preview Download |
|
md5:7eed505a57a1cb74a36760adbee9b3b0
|
903.6 MB | Preview Download |
|
md5:ce6bc386389d491251789c9c552f3543
|
89.3 MB | Preview Download |
|
md5:a90e3d5aa43959c39438e6df218998b4
|
2.4 MB | Preview Download |
|
md5:79371d9a488c7c819da32ba3397cd297
|
66.4 MB | Preview Download |
|
md5:49b48567c8653fbb614914edb21c6236
|
416.1 MB | Preview Download |
|
md5:c2bbe07fd20d7aba6348bdd6e3f234be
|
40.9 MB | Preview Download |
|
md5:4d280e2c0610d3cb846cf040541089ce
|
3.9 MB | Preview Download |
|
md5:32dcb354070e72f3833134f876944ad1
|
173.8 MB | Preview Download |
|
md5:4c0769fa381c4ec2d243ba4eefb8a8c2
|
615.3 MB | Preview Download |
|
md5:b145145c16df5079025d48d7b045c0ae
|
60.8 MB | Preview Download |
|
md5:b97c83a0812712c202cea268411398ce
|
6.3 MB | Preview Download |
|
md5:b9fdde28ba46be74d42c45da1459a491
|
243.7 MB | Preview Download |
|
md5:9123b56d6e5cbecef334eeb14bd3b53a
|
994.9 MB | Preview Download |
|
md5:4e8b75173dce418ba60671a25fe7cf2e
|
98.1 MB | Preview Download |
|
md5:40d54061c8b247207220a42cd33f2034
|
6.1 MB | Preview Download |
|
md5:5b2891b1dd12bba04bea82475a9abffa
|
229.3 MB | Preview Download |
|
md5:5cddda4fdfb0eecf7a80cda2de7a1fe6
|
939.9 MB | Preview Download |
|
md5:e825e6e85ff57736be26ccac9cef2e42
|
92.6 MB | Preview Download |