Project description:These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from bioprinted iPSC-derived human kidney organoids differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). The data contains >2000 cells that passed our QC. Data was used to confirm that bioprinted organoids contain a similar cellular composition as standard manually produced organoids - See https://www.biorxiv.org/content/10.1101/505396v1.
Project description:We compared kidney organoids generated manually ('Man') to those generated by bioprinting single cell deposition ('R0') and thin bioprinted lines ('R40').
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.
Project description:Bulk RNA-seq comparison of kidney organoids bioprinted in 3 different conformations with varying starting cell densities. Density is dictated by the ratio of bioprinter tip movement to the amount of extrusion, where higher ratios spread cells over a larger surface area. We compare organoids printed with no movement ('blob', ratio 0) to those with moderate ('line 3', ratio 20) or high movement ('line 1', ratio 40).
Project description:We developed bioprinted tumor organoids linked to real-time growth pattern quantitation via high-speed live cell interferometry (HSLCI). We demonstrate that bioprinting gives rise to 3D organoid structures that preserve histology and gene expression.
Project description:Human iPSC-derived kidney organoids have the potential to revolutionize discovery, but assessing their consistency and reproducibility across iPSC lines, and reducing the generation of off-target cells remain an open challenge. Here, we used single cell RNA-Seq (scRNA-Seq) to profile 450,118 cells to show that organoid composition and development are comparable to human fetal and adult kidneys. Although cell classes were largely reproducible across iPSC lines, time points, protocols, and replicates, cell proportions were variable between different iPSC lines. Off-target cell proportions were the most variable. Prolonged in vitro culture did not alter cell types, but organoid transplantation under the mouse kidney capsule diminished off-target cells. Our work shows how scRNA-seq can help score organoids for reproducibility, faithfulness and quality, that kidney organoids derived from different iPSC lines are comparable surrogates for human kidney, and that transplantation enhances their formation by diminishing off-target cells.