Enhancing human kidney organoid differentiation from pluripotent stem cells with high-throughput automation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA431788 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6514820_1.fastq.gz | Fastqsanger.gz | |||
| SRR6514820_2.fastq.gz | Fastqsanger.gz | |||
| SRR6514821_1.fastq.gz | Fastqsanger.gz | |||
| SRR6514821_2.fastq.gz | Fastqsanger.gz | |||
| SRR6514818_1.fastq.gz | Fastqsanger.gz |
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Project description:The kidney organoid differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. The cells are grown in a monolayer in a dish for seven days and are subjected to growth factors before being pelleted on day seven. The organoids then continue to differentiate as a 3D structure, with at least 8 distinct kidney cell types identifiable around day 18. Here the EPCAM+ epithelial fraction was isolated from day 25 kidney organoids using MACS-enrichment and RNA-sequencing libraries generated.
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Project description:The kidney organoid differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. The cells are grown in a monolayer in a dish for seven days and are subjected to growth factors before being pelleted on day seven. The organoids then continue to differentiate as a 3D structure, with at least 8 distinct kidney cell types identifiable around day 18. Here proximal tubules were isolated from day 25 kidney organoids and RNA-sequencing libraries generated.
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Project description:The kidney differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. The cells are grown in a monolayer in a dish for seven days and are subjected to growth factors before being pelleted on day seven. The organoids then continue to differentiate as a 3D structure, with at least 8 distinct kidney cell types identifiable around day 18. Here we investigate the reproducibility of the kidney differentiation protocol using RNA sequencing from day 18 organoids. Organoid differentiations were performed in separate batches, and within one of the batches, from three separate vials. The resulting RNA-seq data was analysed to identify genes with highly variable expression between batches and vials.
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Project description: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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