Collections / Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis [Spatial Transcriptomics]

Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis [Spatial Transcriptomics]

Objective: To spatially resolve the identified celltypes, subtypes and transcriptomic profiles from single-nuclei RNA-seq with matched 12 infrapatellar fat pad of knee OA patients using spatial transcriptomics sequencing.

Datasets12
Size~422 MB
AssayVisium
Samplehuman · infrapatellar fat pad
KindOther
PMID:39919907 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse253199")
coll.ordered_artifacts.df()                 # the 12 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
Human infrapatellar fat pad
GSM8016272
human infrapatellar fat pad osteoarthritis, knee 34 MB 2,675 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size34 MB
Obs2,675
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016282
human infrapatellar fat pad osteoarthritis, knee 22 MB 2,341 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size22 MB
Obs2,341
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016273
human infrapatellar fat pad osteoarthritis, knee 37 MB 3,246 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size37 MB
Obs3,246
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016280
human infrapatellar fat pad osteoarthritis, knee 28 MB 2,058 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size28 MB
Obs2,058
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016276
human infrapatellar fat pad osteoarthritis, knee 43 MB 2,200 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size43 MB
Obs2,200
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016274
human infrapatellar fat pad osteoarthritis, knee 27 MB 4,261 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size27 MB
Obs4,261
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016283
human infrapatellar fat pad osteoarthritis, knee 34 MB 3,034 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size34 MB
Obs3,034
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016278
human infrapatellar fat pad osteoarthritis, knee 26 MB 3,085 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size26 MB
Obs3,085
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016281
human infrapatellar fat pad osteoarthritis, knee 48 MB 3,855 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size48 MB
Obs3,855
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016275
human infrapatellar fat pad osteoarthritis, knee 46 MB 3,534 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size46 MB
Obs3,534
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016277
human infrapatellar fat pad osteoarthritis, knee 36 MB 3,163 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size36 MB
Obs3,163
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human infrapatellar fat pad
GSM8016279
human infrapatellar fat pad osteoarthritis, knee 40 MB 2,996 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueinfrapatellar fat pad
Conditionosteoarthritis, knee
Size40 MB
Obs2,996
silver H&E NCBI GEO policy Open in Vitessce

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