Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analysis of cardiomyocyte differentiation from human induced pluripotent stem cells (hiPSCs) in 2D and 3D culture

ABSTRACT: Transcriptomic analysis of cardiomyocyte differentiation from human induced pluripotent stem cells (hiPSCs) in 2D and 3D culture

PROVIDER: PRJNA479439 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7467180.fastq.gz	Fastqsanger.gz
	SRR7467190.fastq.gz	Fastqsanger.gz
	SRR7467200.fastq.gz	Fastqsanger.gz
	SRR7467210.fastq.gz	Fastqsanger.gz
	SRR7467220.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 62

Similar Datasets

Transcriptomic analysis of cardiomyocyte differentiation from human induced pluripotent stem cells (hiPSCs) in 2D and 3D culture

Project description:Tridimensional cardiac differentiation from hiPSCs has been largely described in the literature. However, the exact impact that 3D culture has throughout the entire process of cardiac differentiation remains poorly defined. We developed a robust and efficient 3D platform for cardiomyocyte differentiation from hiPSCs, based on the temporal modulation of WNT signalling using small molecules. 3D aggregates of hiPSCs were generated by forced aggregation in microwells and subsequently differentiated. In order to determine the differences in gene expression profile due to 3D culture throughout the different stages of cardiac differentiation, we compared transcriptional changes between cells in 3D aggregates and standard 2D monolayer cardiac differentiation. Analysis of these data suggests a faster commitment of hiPSCs toward the cardiac lineage and also higher degree of cardiomyocyte functional maturation after 20 days of culture in the 3D aggregates when compared with the 2D monolayer.

2019-06-24 | GSE116574 | GEO

3D Laparoscopy Versus 2D Laparoscopy

Project description:* To compare surgical and oncological outcomes in patients underwent to colorectal resection with 3D vs 2D laparoscopic technique. * To evaluate the visual overload in surgeons using 3D laparoscopic technique.

| 2220465 | ecrin-mdr-crc

3D vs . 2D culture of HUASMC

Project description:3D vs . 2D culture of HUASMC

| PRJNA552084 | ENA

Expression profiling of MCF10A cells in 2D and 3D culture

Project description:In these microarray experiments, we characterize the gene expression of mammary epithelial cells (MCF10A cells) grown in either a traditional monolayer cell culture setting (2D) or on Matrigel, which induces single MCF10A cells to form organized acinar structures (3D). Morphogenesis of mammary epithelial cells into organized acinar structures in vitro is accompanied by widespread changes in gene expression patterns, including a substantial decrease in expression of Myc. The purpose of this study was to analyze the impact of morphogenesis and organization on gene expression with respect to changes in overall gene expression and Myc target gene expression. MCF10A cells were cultured in 2D for either 2 or 5 days (3 biological replicates each) or in 3D for 8 or 16 days (3 or 5 biological replicates, respectively)

2011-06-01 | E-GEOD-26148 | biostudies-arrayexpress

Clinical randomized study of 3D and 2D laparoscopic radical resection for colorectal cancer.

Project description:Interventions: 2D group:2D laparoscopic surgery;3D group:3D laparoscopic surgery Primary outcome(s): operation time;The amount of bleeding;Number of lymph nodes;Postoperative gastrointestinal function recovery time;Postoperative complications Study Design: Randomized parallel controlled trial

| 2663755 | ecrin-mdr-crc

3D vs . 2D culture of HUASMC

Project description:To study the impact of the organotypic assembly of vascular smooth muscle cells on their transcriptome, we cultured human umbilical artery smooth muscle cells under 2D conditions and as aggregates in hanging drops under 3D conditions. After 48 hours, RNA was isolated from both groups

2019-12-16 | GSE133650 | GEO

Expression data of two human cancer cell lines cultivated in 2-dimensional (2D) vs. 3-dimensional (3D) cell culture

Project description:3D cultivation of cells lead to changes in morphology of the cells. This is likely to explain the higher radioresistance of cells growing in 3D compared to cells growing in 2D cell culture. Whole genome gene expression is performed to determine genes involved in changes of cell moroholgy and radioresistance. Keywords: comparison of 2D vs. 3D cell culture RNA of cells was isolated four days after growing in the two different cell culture systems

2010-07-30 | E-GEOD-17347 | biostudies-arrayexpress

Transcription profiling of 25 breast cancer cell lines grown in 2D and 3D tissue culture conditions

Project description:A comparison of gene expression profiles for 25 breast cancer cell lines grown in 2D and 3D tissue culture conditions

2007-05-02 | E-TABM-244 | biostudies-arrayexpress

Expression data of control-shRNA and SATB1-shRNA expressing MDA-MB-231 cells from 2D and 3D culture system

Project description:We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells. Keywords: Comparative studies on Control_shRNA and SATB1_shRNA1 expressing MDA-MB-231 from 2D or 3D culture. We examined control_shRNA-MDA-MB-231 cells and SATB1_shRNA1-MDA-MB-231 cells under two culture condition;on plastic dish(2D culture) and on Matrigel coated dish(3D culture). When SATB1 was depleted by RNAi technology, these normally aggressive cells exhibited normal breast like morphology on 3D. We used two different microarray platforms (Codelink and Affymetrix) to make expression data. Initial analysis of data and cross-platform comparison were performed using Codelink expression analysis and GeneSpring software. We provide ratio for control_shRNA/SATB1_shRNA1-MDA-MB-231 cells for 2D and 3D on this series.

2010-05-26 | E-GEOD-5417 | biostudies-arrayexpress

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). 29 samples total: 2D and 3D control (untreated) in quadruplicate, respectively; 2D and 3D + HGF in quadruplicate, respectively; 2D + HGF + PD-98059 in quadruplicate; 3D + HGF + PD-98059 in triplicate; 2D + HGF + U0126 in triplicate; and 3D + HGF + U0126 in triplicate.

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