Collections / geo-gse207843

geo-gse207843

Datasets18

Size~266 MB

AssayDBiT-seq

Samplemouse · multiple

KindPublication

Flag a data issue

10.1038/s41467-023-37111-w ↗

Download the whole collection

Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse207843")
cohort.members        # the 18 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-gse207843")
coll.ordered_artifacts.to_dataframe()   # the 18 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-gse207843 --dest data/

Install (Python 3.12+) Docs →

Licenses: 18 NCBI GEO policy

About the study

Spatial transcriptomics using multiplexed deterministic barcoding in tissue.

Spatially resolved transcriptomics of tissue sections enables advances in fundamental and applied biomedical research. Here, we present Multiplexed Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm<sup>2</sup> with a 50 µm resolution. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared to previous reports. Furthermore, the introduction of alignment markers allowed seamless registration of images and spatial transcriptomic spots. Together with technological advances, we provide an open-source computational pipeline to prepare raw sequencing data for downstream analysis. The functionality of xDBiT was demonstrated by acquiring 16 spatially resolved transcriptomic datasets from five different murine organs, including the cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of spatial transcriptomes allowed for in-depth characterization of the murine kidney.

Member datasets · 18

DBiT-seq

Mouse heart

GSM6320943

mouse heart 14.6 MB 1,296 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissueheart

Size14.6 MB

Pixels1,296

bronze NCBI GEO policy

DBiT-seq

Mouse kidney

GSM6320946

mouse kidney 19.9 MB 1,293 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuekidney

Size19.9 MB

Pixels1,293

bronze NCBI GEO policy

DBiT-seq

Mouse liver

GSM6320937

mouse liver 18.1 MB 1,295 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissueliver

Size18.1 MB

Pixels1,295

bronze NCBI GEO policy

DBiT-seq

Mouse kidney

GSM6320939

mouse kidney 20.2 MB 1,292 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuekidney

Size20.2 MB

Pixels1,292

bronze NCBI GEO policy

DBiT-seq

Mouse kidney

GSM6320945

mouse kidney 22.2 MB 1,296 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuekidney

Size22.2 MB

Pixels1,296

bronze NCBI GEO policy

DBiT-seq

Mouse cerebellum

GSM6320948

mouse cerebellum 18.9 MB 1,296 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuecerebellum

Size18.9 MB

Pixels1,296

bronze NCBI GEO policy

DBiT-seq

Mouse pancreas

GSM6934375

mouse pancreas 3.0 MB 1,258 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuepancreas

Size3.0 MB

Pixels1,258

bronze NCBI GEO policy

DBiT-seq

Mouse kidney

GSM6320938

mouse kidney 21.9 MB 1,291 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuekidney

Size21.9 MB

Pixels1,291

bronze NCBI GEO policy

DBiT-seq

Mouse heart

GSM6320942

mouse heart 13.2 MB 1,296 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissueheart

Size13.2 MB

Pixels1,296

bronze NCBI GEO policy

DBiT-seq

Mouse cerebellum

GSM6320947

mouse cerebellum 14.9 MB 1,296 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuecerebellum

Size14.9 MB

Pixels1,296

bronze NCBI GEO policy

DBiT-seq

Mouse spleen

GSM6320933

mouse spleen 15.1 MB 1,218 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuespleen

Size15.1 MB

Pixels1,218

bronze NCBI GEO policy

DBiT-seq

Mouse heart

GSM6320935

mouse heart 13.6 MB 1,293 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissueheart

Size13.6 MB

Pixels1,293

bronze NCBI GEO policy

DBiT-seq

Mouse pancreas

GSM6934374

mouse pancreas 2.4 MB 1,214 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuepancreas

Size2.4 MB

Pixels1,214

bronze NCBI GEO policy

DBiT-seq

Mouse spleen

GSM6320940

mouse spleen 16.9 MB 1,271 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuespleen

Size16.9 MB

Pixels1,271

bronze NCBI GEO policy

DBiT-seq

Mouse liver

GSM6320944

mouse liver 11.5 MB 1,295 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissueliver

Size11.5 MB

Pixels1,295

bronze NCBI GEO policy

DBiT-seq

Mouse spleen

GSM6320934

mouse spleen 14.2 MB 1,291 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuespleen

Size14.2 MB

Pixels1,291

bronze NCBI GEO policy

DBiT-seq

Mouse spleen

GSM6320941

mouse spleen 14.2 MB 1,285 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissuespleen

Size14.2 MB

Pixels1,285

bronze NCBI GEO policy

DBiT-seq

Mouse heart

GSM6320936

mouse heart 11.7 MB 1,296 pixels bronze NCBI GEO policy

TechnologyDBiT-seq

Organismmouse

Tissueheart

Size11.7 MB

Pixels1,296

bronze NCBI GEO policy

Cite this collection

No linked publication found — please cite the data source.