Collections / Spatially resolved atlas of IPF fibroblastic foci identifies that PAK2 kinase activation is involved in fibrogenesis

Spatially resolved atlas of IPF fibroblastic foci identifies that PAK2 kinase activation is involved in fibrogenesis

Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease characterized by progressive fibrosis of the lung parenchyma. To identify potential therapeutic targets for IPF, we conducted spatial transcriptomic analysis and single-cell RNA sequencing (scRNA-seq). Our findings reveal that PAK plays a critical role in the immature fibroblast niche during fibrogenesis, highlighting its potential as a therapeutic target for the treatment of IPF.

Datasets9
Size~216 MB
AssayVisium
Samplehuman · lung
KindReplicates
PMID:40675771 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse285246")
coll.ordered_artifacts.df()                 # the 9 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 · 9
Open in Vitessce
Visium
Human lung
GSM8699172
human lung obsolete idiopathic pulmonary fibrosis 24 MB 2,459 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size24 MB
Obs2,459
Magnificationother · 4.051 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8699173
human lung obsolete idiopathic pulmonary fibrosis 23 MB 2,130 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size23 MB
Obs2,130
Magnificationother · 4.050 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8699166
human lung obsolete idiopathic pulmonary fibrosis 36 MB 3,642 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size36 MB
Obs3,642
Magnificationother · 4.050 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8699165
human lung obsolete idiopathic pulmonary fibrosis 23 MB 2,899 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size23 MB
Obs2,899
Magnificationother · 3.682 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8699170
human lung obsolete idiopathic pulmonary fibrosis 26 MB 2,413 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size26 MB
Obs2,413
Magnificationother · 4.050 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8699171
human lung obsolete idiopathic pulmonary fibrosis 23 MB 2,386 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size23 MB
Obs2,386
Magnificationother · 4.050 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8699168
human lung obsolete idiopathic pulmonary fibrosis 21 MB 1,982 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size21 MB
Obs1,982
Magnificationother · 4.049 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8699167
human lung obsolete idiopathic pulmonary fibrosis 24 MB 2,160 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size24 MB
Obs2,160
Magnificationother · 4.050 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8699169
human lung obsolete idiopathic pulmonary fibrosis 17 MB 1,452 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionobsolete idiopathic pulmonary fibrosis
Size17 MB
Obs1,452
bronze H&E Open in Vitessce

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