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~189 MB
AssayVisium
Samplehuman · ovary
KindReplicates
PMID:36882687 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse227019")
coll.ordered_artifacts.df()                 # the 6 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 · 6
Open in Vitessce
Visium
Human ovary
GSM7090087
human ovary ovarian cancer 23 MB 2,567 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size23 MB
Obs2,567
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090085
human ovary ovarian cancer 30 MB 1,979 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size30 MB
Obs1,979
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090083
human ovary ovarian cancer 45 MB 2,770 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size45 MB
Obs2,770
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090086
human ovary ovarian cancer 39 MB 2,584 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size39 MB
Obs2,584
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090084
human ovary ovarian cancer 23 MB 2,558 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size23 MB
Obs2,558
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7090088
human ovary ovarian cancer 30 MB 1,977 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian cancer
Size30 MB
Obs1,977
Magnificationother · 3.364 µm/px
bronze H&E Open in Vitessce

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