|
| Status |
Public on Oct 13, 2018 |
| Title |
Comparative analysis of kidney organoid and adult human kidney single cell and single nucleus transcriptomes |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We analyzed single cell transcriptomes over 80,000 cells isolated from 65 organoids differentiated from iPSCs and ESCs using two different protocols. We find that both protocols generate kidney organoids that contain a diverse range of kidney cells at differing ratios as well as non-renal cell types. We reconstructed lineage relationships during organoid differentiation through pseudotemporal ordering, and identified transcription factor networks associated with fate decisions. When comparing to adult human kidney, we reveal immaturity of all kidney organoid cell types. These results define impressive kidney organoid cell diversity, identify incomplete differentiation as a major roadblock for current directed differentiation protocols and provide a human adult kidney snRNA-seq dataset against which to benchmark future progress.
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| |
|
| Overall design |
Dropseq and 10X Chromium were used to profile organoid cells and adult kidney nuclei
|
| |
|
| Contributor(s) |
Humphreys BD |
| Citation(s) |
30449713 |
| Submission date |
Aug 06, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Haojia Wu |
| E-mail(s) |
haojiawu@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Renal Division/Internal Medicine
|
| Lab |
Humphreys Lab
|
| Street address |
600 S Euclid Ave
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
MO 63110 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (25)
|
|
| Relations |
| BioProject |
PRJNA484783 |
| SRA |
SRP156469 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE118184_BDNF_inhibitor.dge.txt.gz |
5.8 Mb |
(ftp)(http) |
TXT |
| GSE118184_Human_kidney_snRNA.dge.txt.gz |
9.8 Mb |
(ftp)(http) |
TXT |
| GSE118184_Morizane_ES.dge.txt.gz |
9.5 Mb |
(ftp)(http) |
TXT |
| GSE118184_Morizane_iPS_Batch1_2.dge.txt.gz |
20.0 Mb |
(ftp)(http) |
TXT |
| GSE118184_Morizane_iPS_Batch3.dge.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
| GSE118184_Organoid.combined.dge.txt.gz |
91.4 Mb |
(ftp)(http) |
TXT |
| GSE118184_Takasato.iPS.timecourse.txt.gz |
10.9 Mb |
(ftp)(http) |
TXT |
| GSE118184_Takasato_ES.dge.txt.gz |
22.9 Mb |
(ftp)(http) |
TXT |
| GSE118184_Takasato_iPS_Batch1_2.dge.txt.gz |
25.5 Mb |
(ftp)(http) |
TXT |
| GSE118184_Takasato_iPS_Batch3.dge.txt.gz |
6.6 Mb |
(ftp)(http) |
TXT |
| GSE118184_Takasato_iPS_day34.dge.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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