HCA Data Explorer

Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids

Updated August 30, 2022

These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from three biological replicates from the embryonic day (E)18.5 developing mouse kidney and three biological replicates of iPSC-derived human kidney organoids differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). When aggregated, the mouse data represents >6000 cells that passed our QC, containing most major cell types known to exist in the developing mouse kidney. The aggregated human organoid data contains of >7000 cells that passed our QC and contains populations representing endothelial cells, podocytes, stroma, nephron, and off-target populations with similarity to neurons.

Luke ZappiaMurdoch Childrens Research Institute
Luke Zappia (Experimental Scientist)1
1Murdoch Childrens Research Institute
Parisa Nejad
Schwartz Rachel

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/7b947aa2-43a7-4082-afff-222a3e3a4635

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

GEO Series Accessions:

Downloaded and exported data is governed by the HCA Data Release Policy and licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information please see our Data Use Agreement.

Analysis Portals

None

Project Label

DevelopingMouseKidneyHumanKidneyOrganoids

Species

2 species

Sample Type

2 sample types

Anatomical Entity

2 anatomical entities

Organ Part

2 organ parts

Selected Cell Types

Unspecified

Model Organ

kidney

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

2 development stages

Library Construction Method

10x 3' v2

Nucleic Acid Source

single cell

Paired End

true

Analysis Protocol

MergeOptimusLooms_v1.0.0, Optimus_v5.1.1, Optimus_v5.1.2

File Format

4 file formats

Cell Count Estimate

14.6k

Donor Count

2
bam7 file(s)fastq.gz50 file(s)loom9 file(s)xlsx1 file(s)