Collections / The spatial landscape of gene expression isoforms in tissue sections

The spatial landscape of gene expression isoforms in tissue sections

Mouse brain 10x Genomics Visium Spatial Transcriptomics profiles sequence either with Illumina for standard profiling and Nanopore promethION long read sequencer for full-length profiling.

Datasets3
Size~103 MB
AssayVisium
Samplemouse · multiple
KindOther
PMID:36928528 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse153859")
coll.ordered_artifacts.df()                 # the 3 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Open in Vitessce
Visium
Mouse hippocampal formation
GSM4656180
mouse hippocampal formation 46 MB 2,560 obs silver H&E
TechnologyVisium
Organismmouse
Tissuehippocampal formation
Size46 MB
Obs2,560
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse olfactory bulb
GSM4656181
mouse olfactory bulb 14 MB 918 obs silver H&E
TechnologyVisium
Organismmouse
Tissueolfactory bulb
Size14 MB
Obs918
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse hippocampal formation
GSM4656179
mouse hippocampal formation 43 MB 2,500 obs silver H&E
TechnologyVisium
Organismmouse
Tissuehippocampal formation
Size43 MB
Obs2,500
silver H&E Open in Vitessce

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