Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Understanding the reproducibility and robustness of the kidney organoid differentiation protocol using RNA-seq

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE89044 | GEO | 2018/10/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA-Seq profiling of days 0, 7 and 18 kidney organoids differentiated from three separate vials of starting material

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. This data has been generated to investigate the reproducibility of the kidney differentiation protocol using RNA sequencing from days 0, 7 and 18 organoids. Organoid differentiations were performed in parallel from three separate vials of starting material. The resulting RNA-seq data was analysed to identify genes with highly variable expression between vials.

2018-10-31 | GSE99469 | GEO

RNA-Seq profiling of day 7 and day 18 kidney organoids differentiated in two batches

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. This data has been generated to investigate the reproducibility of the kidney differentiation protocol using RNA sequencing from day 18 organoids. Organoid differentiations were performed in two separate batches separated in time. The resulting RNA-seq data was analysed to identify genes with highly variable expression between batches.

2018-10-31 | GSE99468 | GEO

Gene expression profiling of human iPSC kidney organoid-derived proximal tubules

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.

2018-10-31 | GSE99582 | GEO

Gene expression profiling of human iPSC kidney organoid-derived epithelium

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.

2018-10-31 | GSE107305 | GEO

LC MS/MS of kidney organoids during differentiation from day 21 to 29

Project description:Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. Here, we analyzed the organoid proteome trajectory during differentiation. Genes involved in podocytopathies and cystic kidney diseases were abundantly expressed on protein level, distinguishing organoids from almost every available cell culture model. On their pathway to terminal differentiation, organoids developed increased deposition of extracellular matrix. Single cell transcriptomic analysis suggests that most changes locate to podocytes and early podocyte progenitors. This matrix deposition is different from commonly used animal models of glomerular disease. We grew organoids from two independent batches according to the Freedman protocol, and performed proteomic profiling (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. From day 21 of the culture they were used in our experiments up until day 29, where off-target differentiation of organoids becomes an issue.

2023-05-12 | PXD029716 | Pride

Proteome analysis of kidney organoid cells during TNFa stimulation

Project description:Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. Here, we analyzed the organoid proteome after treatment of organoids with 5ng/mL TNFalpha for 24h and 48h compared with vehicle control (VC). Incubation of organoids (day 25 of differentiation) with TNFalpha led to an activation of NFkappaB signaling, and, interestingly, secretion of cytokines and complement components, alongside with extracellular matrix components. Interestingly, this signaling system directly links inflammatory signaling, production of cytokines and complement; and production of extracellular matrix. Thus, we provide a repository of kidney organoid proteins that revealed the potential to model pathophysiological pathways beyond genetic diseases. Organoids were grown according to the Freedman protocol (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. We started TNFa stimulation at day 25, with the 24h stimulation ending on day 26 and the 48h stimulation ending on day 27. We chose day 25 because it lies centrally in the day 21 to day 29 window, where we observe reproducible spheroids with limited off-target differentiation of organoids, which becomes an issue after day 29.

2023-05-12 | PXD029718 | Pride

Proteomic analysis of kidney organoid supernatant during TNFa stimulation

Project description:Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. Here, we analyzed the organoid proteome after treatment of organoids with 5ng/mL TNFalpha for 24h and 48h compared with vehicle control (VC). Incubation of organoids (day 25 of differentiation) with TNFalpha led to an activation of NFkappaB signaling, and, interestingly, secretion of cytokines and complement components, alongside with extracellular matrix components. Interestingly, this signaling system directly links inflammatory signaling, production of cytokines and complement; and production of extracellular matrix. Thus, we provide a repository of kidney organoid proteins that revealed the potential to model pathophysiological pathways beyond genetic diseases. Organoids were grown according to the Freedman protocol (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. We started TNFa stimulation at day 25, with the 24h stimulation ending on day 26 and the 48h stimulation ending on day 27. We chose day 25 because it lies centrally in the day 21 to day 29 window, where we observe reproducible spheroids with limited off-target differentiation of organoids, which becomes an issue after day 29.

2023-05-12 | PXD029696 | Pride

Single cell RNA-Seq of four human kidney organoids

Project description:These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from four biological replicates of iPSC-derived human kidney organoids, in two batches, differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). The aggregated human organoid data contains populations representing endothelial cells, podocytes, stroma, nephron, and off-target populations with similarity to neurons.

2018-12-07 | GSE114802 | GEO

Proteomic analysis of induced pluripotent stem cell-derived kidney organoids

Project description:Kidney organoids were generated from a control iPSC line using a previously published protocol (https://doi.org/10.1038/nprot.2016.098). Organoids were collected at three timepoints during the protocol (day 14, 18 and 25) and prepared for proteomic analyses. The focus of the study was to define the proteomic composition of kidney organoids during differentiation with a particular emphasis on the extracellular matrix and its comparison to in vivo systems. Following a ample fractionation and matrix enrichment strategy, samples were prepared for high resolution label-free tandem mass spectrometry to define the proteomic composition of human kidney organoids.

2021-10-13 | PXD025838 | Pride

Homo sapiens

Project description:RNA-Seq profiling of day 7 and day 18 kidney organoids differentiated in two batches

| PRJNA388553 | ENA