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Series GSE118184 Query DataSets for GSE118184
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.
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
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)
GSM3320174 Takasato_iPS_Batch1
GSM3320175 Takasato_iPS_Batch2
GSM3320176 Takasato_iPS_Batch3_lane1
BioProject PRJNA484783
SRA SRP156469

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
Processed data are available on Series record

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