Collections / Spatial Transcriptomic Activity Atlas of Spinal Sympathetic Neurons Delineates Neural Control of Lipolysis

Spatial Transcriptomic Activity Atlas of Spinal Sympathetic Neurons Delineates Neural Control of Lipolysis

The sympathetic nervous system coordinates the functions of diverse organs to maintain homeostasis and mounts adaptive responses to stressors. Although recent molecular and genetic studies have advanced our understanding of peripheral sympathetic neurons, the spatial and functional organization of spinal sympathetic preganglionic neurons (SPNs) during stress responses remains poorly understood. Here we establish a spatial transcriptomics (STx)-based activity atlas of mouse SPNs under distinct stress conditions. This atlas reveals the spinal segment- and sex-biased organization of SPN transcriptomic subtypes. Using immediate early gene (IEG) induction as a readout of neuronal activation, we found that different stressors, such as cold exposure and glucose deprivation, recruit different SPN transcriptomic subtypes.

Datasets10
Size~65.2 GB
Assay10x Xenium
Samplemouse · spinal cord
KindComparison
Flag a data issue
Python · sddb client
from sddb import Catalog

cohort = Catalog().collection("geo-gse336196")
cohort.members        # the 10 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")
Python · lamindb

Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse336196")
coll.ordered_artifacts.to_dataframe()   # the 10 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse336196 --dest data/

Licenses: 10 NCBI GEO policy

Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829813
mouse spinal cord 1.9 GB 83,912 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size1.9 GB
Cells83,912
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829818
mouse spinal cord 1.8 GB 78,138 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size1.8 GB
Cells78,138
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829814
mouse spinal cord 3.9 GB 172,130 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size3.9 GB
Cells172,130
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829815
mouse spinal cord 3.9 GB 173,341 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size3.9 GB
Cells173,341
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829817
mouse spinal cord 3.4 GB 152,358 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size3.4 GB
Cells152,358
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829816
mouse spinal cord 3.9 GB 167,694 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size3.9 GB
Cells167,694
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829822
mouse spinal cord 12.2 GB 618,208 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size12.2 GB
Cells618,208
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829820
mouse spinal cord 11.0 GB 556,964 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size11.0 GB
Cells556,964
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829821
mouse spinal cord 11.5 GB 591,992 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size11.5 GB
Cells591,992
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse spinal cord
GSM9829819
mouse spinal cord 11.7 GB 598,230 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuespinal cord
Size11.7 GB
Cells598,230
silver NCBI GEO policy Open in Vitessce