Human liver
GSM8291069
human liver breast carcinoma 90.1 MB 2,848 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueliver
Conditionbreast carcinoma
Spots2,848
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~336 MB
AssayVisium
Samplehuman · multiple
KindComparison
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse268427")
cohort.members # the 3 datasets as a table
print(cohort.licenses()) # check the terms before you download
sdatas = cohort.to_dict() # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/") Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse268427")
coll.ordered_artifacts.to_dataframe() # the 3 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse268427 --dest data/Licenses: 3 NCBI GEO policy
Member datasets · 3
Human liver
GSM8291071
human liver breast carcinoma 123 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueliver
Conditionbreast carcinoma
Spots4,992
silver H&E NCBI GEO policy
Human breast
GSM8291070
human breast breast carcinoma 123 MB 4,955 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuebreast
Conditionbreast carcinoma
Spots4,955
silver H&E NCBI GEO policy
Cite this collection
doi.org/10.1038/s42003-024-07043-2 ↗ BibTeX
@article{Wang_2024,
title = {snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives},
volume = {7},
ISSN = {2399-3642},
url = {http://dx.doi.org/10.1038/s42003-024-07043-2},
DOI = {10.1038/s42003-024-07043-2},
number = {1},
journal = {Communications Biology},
publisher = {Springer Science and Business Media LLC},
author = {Wang, Taopeng and Roach, Michael J. and Harvey, Kate and Morlanes, Javier Escudero and Kiedik, Beata and Al-Eryani, Ghamdan and Greenwald, Alissa and Kalavros, Nikolaos and Dezem, Felipe Segato and Ma, Yuling and Pita-Juarez, Yered H. and Wise, Kellie and Degletagne, Cyril and Elz, Anna and Hadadianpour, Azi and Johanneson, Jack and Pakiam, Fiona and Ryu, Heeju and Newell, Evan W. and Tonon, Laurie and Kohlway, Andrew and Drennon, Tingsheng and Abousoud, Jawad and Stott, Ryan and Lund, Paul and Durruthy, Jens and Vallejo, Andres F. and Li, Wenyan and Salomon, Robert and Kaczorowski, Dominik and Warren, Joanna and Butler, Lisa M. and O’Toole, Sandra and Plummer, Jasmine and Vlachos, Ioannis S. and Lundeberg, Joakim and Swarbrick, Alexander and Martelotto, Luciano G.},
year = {2024},
month = Oct
}