Collections / Single-cell and Spatial Transcriptomic Profiling of the Bone Metastatic Microenvironment

Single-cell and Spatial Transcriptomic Profiling of the Bone Metastatic Microenvironment

The goal of this study is to comprehensively characterize the cellular composition, transcriptional programs, and spatial organization of the bone metastatic microenvironment and to assess how therapeutic perturbation influences tumor–microenvironment interactions. A mouse bone metastasis model was established via internal iliac artery injection of Lewis lung carcinoma cells, and metastatic lesions were monitored by in vivo imaging. Single-cell RNA sequencing and 10x Genomics Visium–based spatial transcriptomics were generated from metastatic bone tissues to provide complementary cellular and spatial resolution.

Datasets4
Size~99 MB
AssayVisium
Samplemouse · bone tissue
KindOther
PMID:42108258 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse323357")
coll.ordered_artifacts.df()                 # the 4 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()}
Member datasets · 4
Visium
Mouse bone tissue
GSM9564257
mouse bone tissue lung carcinoma 29 MB 2,022 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebone tissue
Conditionlung carcinoma
Size29 MB
Obs2,022
bronze H&E
Open in Vitessce
Visium
Mouse bone tissue
GSM9564255
mouse bone tissue lung carcinoma 17 MB 2,212 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebone tissue
Conditionlung carcinoma
Size17 MB
Obs2,212
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse bone tissue
GSM9564258
mouse bone tissue lung carcinoma 25 MB 2,153 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebone tissue
Conditionlung carcinoma
Size25 MB
Obs2,153
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse bone tissue
GSM9564256
mouse bone tissue lung carcinoma 28 MB 1,869 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebone tissue
Conditionlung carcinoma
Size28 MB
Obs1,869
bronze H&E Open in Vitessce

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