Visium Human liver
GSM8291069
human liver breast carcinoma 86 MB 2,848 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueliver
Conditionbreast carcinoma
Obs2,848
silver H&E NCBI GEO policy
Collections / snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profiling [Visium]
snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profiling [Visium]
FFPE tissue samples have long been considered challenging for sc-/sn-RNA sequencing assays. In this study, we developed a novel snRNA-seq workflow, snPATHO-seq, for FFPE tissue samples utilising isolated high-quality nuclei from FFPE samples and 10X Genomics FLEX chemistry. The snPATHO-seq demonstrated consistent performance with the established 10X Genomics 3' assay. In addition, it allows more accurate single-nucleus and spatial transcriptomics integration with the FFPE Visium dataset generated from the same FFPE block. We envision this new protocol can facilitate the transcriptomic interpretation of millions of FFPE archives generated and simplify the sample collection process and data generation.
Datasets3
Size~321 MB
AssayVisium
Samplehuman · multiple
KindComparison
Download the whole collection
Python · lamindb
import lamindb as ln
import spatialdata as sd
coll = ln.Collection.get(key="geo-gse268427")
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()}Member datasets · 3
Visium 
Visium Human liver
GSM8291071
human liver breast carcinoma 118 MB 4,992 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueliver
Conditionbreast carcinoma
Obs4,992
silver H&E NCBI GEO policy
Visium Human breast
GSM8291070
human breast breast carcinoma 117 MB 4,955 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuebreast
Conditionbreast carcinoma
Obs4,955
silver H&E NCBI GEO policy
Cite this collection
No linked publication found — please cite the data source.