Collections / Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

The Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive development. In this study, we compared two platforms Illumina NextSeq 2000 and GeneMind Genolab M for 10x Genomics Visium spatial transcriptomics.

Datasets6
Size~198 MB
AssayVisium
Samplehuman · ovary
KindReplicates
Flag a data issue
PMID:36882687 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse227019")
cohort.members        # the 6 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/")
Install (Python 3.12+) Docs →
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-gse227019")
coll.ordered_artifacts.to_dataframe()   # the 6 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse227019 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 NCBI GEO policy

Member datasets · 6
Open in Vitessce
Visium
Human ovary
GSM7090087
human ovary ovarian cancer 23.6 MB 2,567 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size23.6 MB
Spots2,567
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090085
human ovary ovarian cancer 31.2 MB 1,979 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size31.2 MB
Spots1,979
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090083
human ovary ovarian cancer 46.8 MB 2,770 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size46.8 MB
Spots2,770
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090086
human ovary ovarian cancer 41.1 MB 2,584 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size41.1 MB
Spots2,584
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090084
human ovary ovarian cancer 24.3 MB 2,558 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size24.3 MB
Spots2,558
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090088
human ovary ovarian cancer 30.9 MB 1,977 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size30.9 MB
Spots1,977
Magnificationother · 3.364 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1186/s12864-023-09192-w ↗
BibTeX 
@article{Pavel_2023,
  title = {Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics},
  volume = {24},
  ISSN = {1471-2164},
  url = {http://dx.doi.org/10.1186/s12864-023-09192-w},
  DOI = {10.1186/s12864-023-09192-w},
  number = {1},
  journal = {BMC Genomics},
  publisher = {Springer Science and Business Media LLC},
  author = {Pavel, Iamshchikov and Irina, Larionova and Tatiana, Gerashchenko and Denis, Piankov and Philipp, Koshkin and Sergei, Korostelev and Evgeny, Denisov},
  year = {2023},
  month = Mar
}