GEO DataSets

(Submitter supplied) We developed novel chemically defined recipe media named NPSR-v2, that was capable of expanding mouse and human nephron progenitor cells (NPC) for long term culture in vitro in 2D (2 Dimension) format. NPSR-v2 and these expanded NPC can be used for versatile application, such as reprograming, whole genome-wide CRISPR screen, kidney-associated disease modeling and library drug screening etc.

Organism:

Homo sapiens; Mus musculus; synthetic construct

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

63 Samples

Download data: XLSX

(Submitter supplied) Nephron progenitor cells (NPCs) self-renew and differentiate into nephrons, the functional units of the kidney. Here we report manipulation of p38 and YAP activity creates a synthetic niche that allows the long-term clonal expansion of primary mouse and human NPCs, and induced NPCs (iNPCs) from human pluripotent stem cells. Cultured iNPCs resemble closely primary human NPCs, generating nephron organoids with abundant distal convoluted tubule cells, which are not observed in published kidney organoids. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

4 Samples

Download data: H5, TBI, TSV

(Submitter supplied) Podocytes play an important filtration role in the kidney. We examined culture condition for efficient podocyte induction and established a method to selectively induce podocytes from human iPS cells. To understand how expression profiles of human iPS cell-derived podocytes were close to that in vivo, we isolated human adult podocytes for human adult kidney. Purified RNAs from human iPS cells, nephron progenitor cells, human immortalized podocyte cell line, human iPS cell-derived podocytes, and sorted human adult podocytes were analyzed by RNA-seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: XLSX

(Submitter supplied) In order to characterize and benchmark the podocytes-like cells generated through human ES cell differentiation, we generated transcriptional profiles of renal corpuscles from embryonic human kidneys using RNA-Seq. To compare, we also performed RNA-Seq of human immortalized podocyte cell lines before and after thermoswitch.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: XLSX

(Submitter supplied) To study the developmental process of human podocytes and compare to the in vitro counterpart, we dissociated cells from the inner and outer kidney cortex as well as kidney organoids, and performed 10X Genomics single-cell RNA sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TAR

(Submitter supplied) To assess in vitro derived podocytes, we examined the transcriptional changes during human podocyte development and applied that knowledge to pinpoint strengths and limitations of hESC-derived podocytes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

31 Samples

Download data: TXT

(Submitter supplied) A critical event during kidney organogenesis is the differentiation of podocytes, specialized epithelial cells that filter blood plasma to form urine. Podocytes derived from human pluripotent stem cells (hPSC-podocytes) have recently been generated in nephron-like kidney organoids, but the developmental stage of these cells and their capacity to reveal disease mechanisms remains unclear. Here, we show that hPSC-podocytes phenocopy mammalian podocytes at the capillary loop stage (CLS), recapitulating key features of ultrastructure, gene expression, and mutant phenotype. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) During development, nephron progenitor forming one million nephrons, a functional unit in the kidney. However, nephron progenitor ceases before birth in human when they terminally differentiated to the nephron. Our lab established the method for induction of nephron progenitors from mouse Embryonic Stem (ES) cells and/or human induced Pluripotent Stem Cells (iPSCs) (Taguchi et al., Cell Stem Cell. 2014, 2017). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: XLSX

(Submitter supplied) We performed RNA-Seq on wildtype or PDK2-null human kidney organoids treated with various concentration of QNZ or control. For WT organoid we started QNZ treatment on day8 and harvested the samples on day28. For PKD2 null organoids we started treatment on day13 and harvested the samples on day20 We performed RNA-Seq on PDK2-null human organoid derived cysts treated with various concentration of QNZ or control. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

36 Samples

Download data: CSV

(Submitter supplied) Human pluripotent stem cell-derived organoids are models for human development and disease. We report a modified human kidney organoid system that generates thousands of similar kidney organoids, each consisting of 1 to 2 nephron-like structures. Single-cell transcriptomic profiling and immunofluorescence validation highlighted patterned nephron-like structures, utilizing similar pathways, with distinct morphogenesis, to human nephrogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: TAR

(Submitter supplied) Analysis of induced nephron progenitor cells from female/male urine cells (iNPC-F/INPC-M) by defined transcription factors vs. ESC derived nephron progenitor cell (ESC-NPC_H9/ESC-NPC_BG01) and female/male urine cells (UC-F/UC-M). Results provide insight into molecular similarities between induced nephron progenitor cells and human ESC derived nephron progenitor cell

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) Purpose: Nephron progenitor cells generate nephrons, the basic units of kidney. We developed methods to culture mouse and human NPCs in their self-renewal state in vitro with full nephrogenic potentials. The RNA-seq here is used to compare the global gene expression of long-term cultured mouse NPCs and their cognate freshly isolated primary NPCs Methods: mRNA profiles were generated by deep sequencing in duplicate from E11.5, E12.5, E13.5, E16.5 and P1 primary NPCs, and from long-term cultured NPCs derived from E11.5, E13.5, E16.5 and P1 (Passage 20 and Passage 80 for each cell line). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

29 Samples

Download data: XLS

(Submitter supplied) 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.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

3 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

3 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) The kidney differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. Initially the cells are grown in a monolayer in a dish before being pelleted on day seven. We have performed RNA sequencing on three replicates taken at two points before cells are pelleted: day 0, when they are still iPSCs, and day 4 when cells have been exposed to growth factors and have started differentiating.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) A platform for generating expandable, branching and gene-editable ureteric bud organoid from primary mouse and human ureteric bud progenitor cells and human pluripotent stem cells, and its maturation into collecting duct organoid.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

10 Samples

Download data: CSV