HCA Data Explorer

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

Access Granted
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

High throughput single cell RNA-seq of developing mouse kidney and human kidney organoids reveals a roadmap for recreating the kidney

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:

Atlas

None

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)