Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of human iPSC kidney organoid-derived epithelium

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE107305 | GEO | 2018/10/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

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

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.

2018-10-31 | GSE89044 | GEO

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 from early time points in the kidney differentiation protocol

Project description: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.

2018-10-31 | GSE88942 | GEO

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

2023-05-12 | PXD029696 | Pride

Transcriptional profiling of mouse molar and incisor tooth organoids

Project description:Organoid models provide powerful tools to study tissue biology and development in a dish. Here, we established first-time organoid models from early-postnatal (postnatal day 7) mouse molar and incisor, capable of differentiation toward ameloblast-like cells in vitro. To more in detail characterise organoids from mouse molar and incisor, bulk RNA-sequencing was performed on the following (1) early passage (passage 0) organoids from both tooth types grown in basal tooth organoid medium (TOM) with or without addition of exogenous epidermal growth factor (EGF); and (2) late passage (passage 5) organoids grown in TOM+EGF or differentiation medium (DM).

2023-04-19 | E-MTAB-12557 | biostudies-arrayexpress

Real-time quantitative PCR analysis of Lentinula edodes mycelium face on different stress treatments.

Project description:L. edodes strain w1 was cultured at 25°C in MYG medium (containing 1% malt extract, 0.1% peptone, 0.1% yeast extract, and 2% glucose). Fresh mycelium blocks were cultured in a 9cm petri dish containing MYG medium. After 8-day dark cul- ture, and they were divided into different treatment groups (group A,B,C,D,E). Group A was treated with 8mm-diameter L. edodes mycelium block on MYG medium for seven days and then treated at 37 °C for 30 min. 3. Group B was treated with 8mm-diameter L. edodes mycelium block on MYG medium for seven days and then treated at 4 °C for 60 min. Group C was treated with 8mm-diameter L. edodes mycelium block on MYG medium for seven days and then under 3500 lx light for 1 h. In group D, 8mm-diameter fresh L. edodes mycelium block were inoculated into MYG medium containing cadmium ions. In group E, 8mm-diameter L. edodes mycelium block was inoculated at 10 mm from the edge of the petri dish, and cultured at 25 ° C for 7 days. Afterwards, an activated 8-mm diameter tricho- derma mycelium block was inoculated at 1 cm from the edge of the petri dish at one end of the petri dish diameter (corresponding to the other end where L. edodes mycelium block was inoculated)

2024-11-25 | GSE219161 | GEO

Single-cell ATAC-seq of human cerebral organoids

Project description:Single cell ATAC-seq (scATAC-seq) was performed at various stages of differentiation of human pluripotent stem cells to 4 month old cerebral organoids. scATAC-seq was performed on the following days of differentiation: day 0 (pluripotent stem cell), day 4 (embryoid body), day 10 (neuroectoderm), day 15 (neuroepithelium), day 30 (1 month old cerebral organoid), day 60 (2 months old cerebral organoid), and day 120 (4 months old cerebral organoid).

2019-10-16 | E-MTAB-8089 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data