Collections / single-cell multiomics data for the developing human pelvic girdle [spatial]

single-cell multiomics data for the developing human pelvic girdle [spatial]

Human pelvic girdle, especially the ilium is considered an evolutionary novelty. To understand the genetic architecute behind the formation of this structure, we conducted single cell multiomics across developmental stages.

Datasets28

Size~531 MB

AssayVisium

Samplehuman · ilium

KindReplicates

Flag a data issue

PMID:40866708 ↗

Download the whole collection

Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse281317")
cohort.members        # the 28 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-gse281317")
coll.ordered_artifacts.to_dataframe()   # the 28 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-gse281317 --dest data/

Install (Python 3.12+) Docs →

Licenses: 28 NCBI GEO policy

Member datasets · 28

Visium

Human ilium

GSM8618670

human ilium 14.7 MB 894 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size14.7 MB

Spots894

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618673

human ilium 15.0 MB 1,007 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size15.0 MB

Spots1,007

Magnificationother · 6.451 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618655

human ilium 24.6 MB 771 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size24.6 MB

Spots771

Magnificationother · 3.187 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618653

human ilium 4.7 MB 152 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size4.7 MB

Spots152

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618652

human ilium 19.7 MB 907 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size19.7 MB

Spots907

Magnificationother · 5.739 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618669

human ilium 37.7 MB 2,308 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size37.7 MB

Spots2,308

Magnificationother · 6.430 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618672

human ilium 8.0 MB 773 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size8.0 MB

Spots773

Magnificationother · 6.442 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618668

human ilium 23.1 MB 2,264 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size23.1 MB

Spots2,264

Magnificationother · 5.778 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618660

human ilium 16.2 MB 478 spots bronze NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size16.2 MB

Spots478

bronze NCBI GEO policy

Visium

Human ilium

GSM8618667

human ilium 31.4 MB 2,310 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size31.4 MB

Spots2,310

Magnificationother · 5.765 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618650

human ilium 29.4 MB 1,386 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size29.4 MB

Spots1,386

Magnificationother · 3.964 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618662

human ilium 11.1 MB 329 spots bronze NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size11.1 MB

Spots329

bronze NCBI GEO policy

Visium

Human ilium

GSM8618661

human ilium 8.4 MB 228 spots bronze NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size8.4 MB

Spots228

bronze NCBI GEO policy

Visium

Human ilium

GSM8618663

human ilium 18.6 MB 784 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size18.6 MB

Spots784

Magnificationother · 3.471 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618654

human ilium 19.7 MB 1,133 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size19.7 MB

Spots1,133

Magnificationother · 3.280 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618651

human ilium 24.5 MB 1,684 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size24.5 MB

Spots1,684

Magnificationother · 5.794 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618659

human ilium 10.7 MB 159 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size10.7 MB

Spots159

Magnificationother · 3.277 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618658

human ilium 9.2 MB 182 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size9.2 MB

Spots182

Magnificationother · 3.470 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618656

human ilium 14.7 MB 436 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size14.7 MB

Spots436

Magnificationother · 3.221 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618646

human ilium 26.1 MB 1,327 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size26.1 MB

Spots1,327

Magnificationother · 3.872 µm/px

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618647

human ilium 16.9 MB 907 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size16.9 MB

Spots907

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618649

human ilium 26.9 MB 1,156 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size26.9 MB

Spots1,156

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618664

human ilium 20.3 MB 856 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size20.3 MB

Spots856

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618648

human ilium 22.0 MB 1,401 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size22.0 MB

Spots1,401

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618665

human ilium 29.8 MB 1,784 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size29.8 MB

Spots1,784

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618666

human ilium 25.1 MB 1,032 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size25.1 MB

Spots1,032

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618671

human ilium 13.7 MB 1,367 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size13.7 MB

Spots1,367

bronze H&E NCBI GEO policy

Visium

Human ilium

GSM8618657

human ilium 8.4 MB 150 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissueilium

Size8.4 MB

Spots150

bronze H&E NCBI GEO policy

Cite this collection

doi.org/10.1038/s41586-025-09399-9 ↗

BibTeX

@article{Senevirathne_2025,
  title = {The evolution of hominin bipedalism in two steps},
  volume = {645},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-025-09399-9},
  DOI = {10.1038/s41586-025-09399-9},
  number = {8082},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Senevirathne, Gayani and Fernandopulle, Serena C. and Richard, Daniel and Baumgart, Stephanie L. and Christensen, Anika Liv and Fabbri, Matteo and Höppner, Jakob and Jüppner, Harald and Li, Peishu and Bothe, Vivien and Fröbisch, Nadia and Simcock, Ian and Arthurs, Owen J. and Calder, Alistair and Freilich, Naomi and Nowlan, Niamh C. and Glass, Ian A. and Craft, April and Capellini, Terence D.},
  year = {2025},
  month = Aug,
  pages = {952–963}
}