Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

2.5D tubulogenesis

ABSTRACT: Hepatocyte growth factor-induced three-dimensional tubulogenesis (3D) is a simple and highly controllable system for studying epithelial tubule initiation and maintenance. However, due to its limited efficiency and asynchronous development, isolating genes associated with specific morphological changes observed during tubule formation has been unfeasible. Here we report a significantly enhanced in vitro culture method called 2.5-dimensional tubulogenesis (2.5D). Detailed image analysis of 2.5D has revealed morphologically distinct stages -- monolayer, extension, and tubule -- and finds that these stages display in a highly synchronized manner. Using time-course transcriptional profiling, we collected genes whose expression changes specifically associate with extension and tubule stage.

ORGANISM(S): Canis lupus familiaris

PROVIDER: GSE25514 | GEO | 2010/12/24

SECONDARY ACCESSION(S): PRJNA133765

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

2.5D tubulogenesis

Project description:Hepatocyte growth factor-induced three-dimensional tubulogenesis (3D) is a simple and highly controllable system for studying epithelial tubule initiation and maintenance. However, due to its limited efficiency and asynchronous development, isolating genes associated with specific morphological changes observed during tubule formation has been unfeasible. Here we report a significantly enhanced in vitro culture method called 2.5-dimensional tubulogenesis (2.5D). Detailed image analysis of 2.5D has revealed morphologically distinct stages -- monolayer, extension, and tubule -- and finds that these stages display in a highly synchronized manner. Using time-course transcriptional profiling, we collected genes whose expression changes specifically associate with extension and tubule stage. Time-course microarrays to identify genes whose temporal regulation is associated with extension and tubule stages. Four biological replicates for each stage (monolayer, extension, and tubule).

2010-12-24 | E-GEOD-25514 | biostudies-arrayexpress

Canis lupus familiaris

Project description:2.5D tubulogenesis

| PRJNA133765 | ENA

2D and 3D Madin-Darby Canine Kidney Cell Type II cell line response to hepatocyte growth factor

Project description:Analysis of 2D (transwell) and 3D (collagen type I) cultured MDCK cells and HGF (a MAPK activator). Traditional 2D cultures are fast and inexpensive but do no mimic natural niche/cell environment as well as the more laborious and costly 3D-cultures. 3D cultures, arguably, are better models for the study of developmental processes, such as tubulogenesis. Epithelial organs (such as kidney) develop via tubulogenesis, a process, at least in part, regulated by MAPK signaling. Therefore, 2D and 3D cells also treated with HGF plus MAPK inhibitors. Results provide insights into differential response to HGF-induced tubulogenesis depending on cell culture conditions (2D vs. 3D).

2014-03-31 | GSE49518 | GEO

Transcription profiling of human umblical vein endothelial cells (HUVEC) undergoing tubulogenesis in a 3D fribrin matrix or cultured as monolayers

Project description:In order to determine genes that are differentially expressed during angiogenesis, Human Umbilical Vein Endothelial Cells (HUVEC) were cultured as 3D cultures undergoing tubulogenesis in a 3D fibrin matrix, or cultured as monolayers on top of a 3D fibrin matrix. RNA was then collected, reverse transcribed to cDNA and hybridized to glass slide oligo arrays containing 19k human genes. Differentially expressed genes in HUVECs undergoing tubulogenesis were then determined by comparing 2D to 3D culture samples.

2009-10-29 | E-MEXP-2410 | biostudies-arrayexpress

Endothelial Cell Morphogenesis

Project description:Human microvascular endothelial cells were stimulated to either proliferate or undergo tubulogenesis over an 8 hour time period. Keywords: Time Series

2006-04-08 | GSE3891 | GEO

Transcriptomic analysis of mouse preimplantation embryo development and nutrient provision

Project description:Purpose: The goals of this study are to define transcriptome (RNA-seq) of mouse preimplantation embryos at different stages of development under a range of different environmental conditions. Methods: Mouse preimplantation embro transcriptional profiles were generated using embryos at several different developmental stages using Smart-seq2. Results: RNA-seq analysis finds that there is a highly dynamic pattern of gene expression during the preimplantation period. The sensitiivty to nutrient conditions varies markedly at different stages of development, with 2C embryos more sensitive to pyruvate omission than later stage embryos. Conclusions: Our study represents a comprehensive analysis of the mouse preimplantation development transcriptome, and how pyruvate provision impacts different developmental stages.

2020-10-14 | GSE159484 | GEO

2D and 3D Madin-Darby Canine Kidney Cell Type II cell line response to hepatocyte growth factor

2014-03-31 | E-GEOD-49518 | biostudies-arrayexpress

Transcription profiling of human microvascular endothelial cells undergoing proliferation or tubulogenesis

Project description:Human microvascular endothelial cells were stimulated to either proliferate or undergo tubulogenesis over an 8 hour time period.

2007-06-22 | E-GEOD-3891 | biostudies-arrayexpress

Transcription profiling of Drosophila pooled Malpighian tubules vs. whole fly

Project description:This is an affymetrix array experiment comparing the transcriptome of the Malpighian tubule (or renal tubule) of 7-day adult Oregon R strain Drosophila melanogaster with matched whole fly samples. It is described in:,Wang, J., Kean, L., Yang, J., Allan, A. K., Davies, S. A., Herzyk, P. and Dow, J. A. T. (2004). Function-informed transcriptome analysis of Drosophila renal tubule. Genome Biol. In press.,There are five tubule samples (each derived from approx 1000 tubules (!)), and 5 matched whole-fly samples. i.e. tubule 2 is dissected from the same vial as WholeFly2.,As the tubule is probably the premier tissue for true physiology in Drosophila, the dataset can usefully be interrogated in conjunction with the detailed physiological understanding of the tissue: see,http://fly.to/tubules

2007-07-06 | E-GEOD-1690 | biostudies-arrayexpress

Bulk RNA-seq analysis of HUVEC cell cultures with Cerebral Cavernous Malformation (CCM) protein knockdown

Project description:Gene expression profiles of WT (wild type) and CCM-1, -2, and -3 KD (knockdown of krit1, ccm2 and pdcd10 genes) cells under 2D (Matrigel-coated plastic) and 3D (Matrigel) conditions. Deep sequencing of RNA was performed for cells at the initial (2hrs) and later (6hrs) stages of EC tubule formation.

2018-11-19 | GSE116323 | GEO

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