Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

110 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human mesenchymal stromal cells cultured in PEG hydrogels with and without FGF-2

ABSTRACT: FGF-2 is commonly used in culture media when growing mechenchymal stromal cells. Here, we cultured human MSCs from 3 donors with and without 50 ng/ml FGF-2 (Prepotech, human recombinant) in 3D PEG hydrogels, and analysed transcriptome changes by RNA sequencing.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Edward Horton

PROVIDER: E-MTAB-8510 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

RNA-seq of mesenchymal stromal cells cultured in the presence of breast cancer cell secretomes

Project description:Mesenchymal stromal cells were cultured in 3D PEG hydrogels for 7 days in the presence of serum-free media or conditioned media from a panel of breast cancer cells (MCF-7, MDA-MB-231, MDA-MB-231 lung-tropic, MDA-MB-231 brain-tropic, MDA-MB-231 bone-tropic). In all cases, the secretomes were collected after cancer cells were in serum-free media for 24h.

2019-05-28 | E-MTAB-6998 | biostudies-arrayexpress

RNA-seq of human mesenchymal stromal cells cultured in PEG hydrogels with and without FGF-2

Project description:RNA-seq of human mesenchymal stromal cells cultured in PEG hydrogels with and without FGF-2

| PRJEB35352 | ENA

E-MTAB-8510

Project description:RNA-seq of human mesenchymal stromal cells cultured in PEG hydrogels with and without FGF-2

2025-01-16 | E-MTAB-8510 | ExpressionAtlas

A microenvironment-inspired synthetic 3D model for pancreatic ductal adenocarcinoma organoids - 3D PEG-CBF-0.5 MS

Project description:LC-MS/MS based analysis of murine PCOs growing in 3D PEG-CBF-0.5 hydrogels for four days.

2021-11-29 | PXD022520 | Pride

RNA-seq of 4T1 mouse breast cancer cells cultured on soft vs stiff polyacrylamide hydrogels for 24 hours

Project description:The tumour microenvironment is a critical element involved in tumour progression and responsiveness to therapies. Using functionalized tunable stiffness hydrogel, mimicking the mechanical properties of healthy and tumour tissues, we explore how the stiffness of the microenvironment can influence cancer cells by generating RNA-seq transcriptional profiles of 4T1 mouse breast cancer cells cultured on soft vs stiff polyacrylamide hydrogels for 24 hours.

2024-12-30 | E-MTAB-11487 | biostudies-arrayexpress

Single cell RNA-seq of hiPSC-derived kidney organoids differentiated within self-assembling peptide hydrogels and the animal-derived matrix Matrigel

Project description:scRNA-seq was used to characterise hiPSC-derived kidney organoids differentiated within fully synthetic self-assembling peptide hydrogels of variable mechanical strengths and compare these to organoids differentiated within the animal-derived matrix, Matrigel. Organoids were matured in the respective matrices until day 24 of differentiation and 6 organoids per support matrix were then pooled and dissociated using the cold-active protease from Bacillus licheniformis. Cells were processed on the 10x Genomics Chromium platform using the Single-Cell 3’ v3.1 protocol. The NextSeq500 (Illumina) was used to sequence the libraries generated and initial processing of the data was carried out using the 10X Genomic Cell Ranger v3.1.0 pipeline.

2022-10-31 | E-MTAB-11149 | biostudies-arrayexpress

A genome-wide analysis of human pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels compared to standard 2D or 3D cell culture platforms

Project description:The influence of 2D and 3D cell culture platforms on vascular function was investigated by comparing gene expression for human pluripotent stem cell-derived endothelial cells (H1-ECs), primary human brain vascular pericytes (pericytes), and human umbilical vein endothelial cells (HUVECs) cultured on tissue culture polystyrene (TCP, “2D”), on or in poly(ethylene glycol) (PEG) hydrogels formed via “thiol-ene” photopolymerization, and on or in gelled Matrigel. ECs cocultured with pericytes in PEG formed vascular networks with global gene expression that was highly correlated to a standard 3D Matrigel assay (Spearman’s coefficients ≥ 0.98). H1-ECs, HUVECs, and pericytes were characterized gene expression signatures associated with the cell cycle and mitosis when cultured on TCP surfaces compared to cells cultured on top of or encapsulated in PEG hydrogels or Matrigel. The proliferative signature was not necessarily a function of the 2D format, since endothelial cells cultured on PEG hydrogels were not characterized by increased proliferation or a proliferative gene signature compared to cells encapsulated in PEG hydrogels. The proliferative phenotype for H1-ECs on TCP was regulated by FAK-ERK activity, and inhibition or knockdown of ERK pathway signaling decreased proliferation and cell cycle genes while increasing expression of “3D-like” vasculature development genes. Our results suggest that cells in 2D culture adopt a highly proliferative state that interferes with normal vascular function and provides unique insight into the importance of cellular and extracellular context for in vitro tissue modeling.

2017-02-22 | GSE93511 | GEO

Cholangiocyte organoid culture in hydrogels from decellularized liver tissue

Project description:Culture of human cholangiocyte organoids in hydrogels derived from healthy liver extracellular matrix (LECM) extracts prepared from decellularized human livers are evaluated in an effort to establish a platform for production of cholangiocyte organoids for clinical regenerative applications. Human intrahepatic cholangiocyte organoids (ICO) grown in hydrogels made from LECM are compared those grown in mouse tumor derived basement membrane extracts (BME). Culture was performed with amino acids labeled with stable heavy isotopes to enable separation of ECM from the hydrogels from that of the produced by the cells with mass spectrometry (MS). MS data were used to evaluate the protein production of ICO comparing the different hydrogel substrates. The study also contains evaluation of the properties of the hydrogel substrates and focuses on expansion and differentiation of the ICO.

2022-04-13 | PXD028417 | Pride

Identification of Poly Ethylene Glycol (PEG) and PEG-based Detergents Using Peptide Search Engines

Project description:Polyethylene glycol (PEG) is one of the most common polymer contaminations in MS samples. At present, the detection of PEG and other polymers relies largely on manual inspection of raw data which is laborious and frequently difficult due to sample complexity and retention characteristics of polymer species in reversed phase chromatography. We developed a new strategy for the automated identification of PEG molecules from MSMS data using protein identification algorithms in combination with a database containing “PEG-proteins”. Through definition of variable modifications, we extend the approach for the identification of commonly used PEG-based detergents. We exemplify the identification of different types of polymers by static nanoESI-MSMS analysis of pure detergent solutions and data analysis using Mascot. Analysis of LC-MSMS runs of a PEG contaminated sample by Mascot identified 806 PEG-spectra originating from four PEG species using a defined set of modifications covering PEG and common PEG-based detergents. Further characterization of the sample for unidentified PEG species using error tolerant and mass tolerant searches resulted in identification of 3409 and 3187 PEG related MSMS spectra, respectively. We further demonstrate the applicability of the strategy for Protein Pilot and MaxQuant.

2018-05-28 | PXD009376 | Pride

Single cell analysis of iPSC-derived cortical organoids in biofunctionalized gelatin hydrogels

Project description:Human neural organoid models have become an important tool for studying neurobiology. In this work, we compared Matrigel to an N-cadherin peptide-functionalized gelatin methacryloyl hydrogel (termed GelMA-Cad) for culturing cortical neural organoids. Specifically, we compare five materials: (1) Matrigel, (2) GelMA-Cad with high crosslinker (HC), (3) GelMA-Cad with low crosslinker (LC), (4) GelMA HC and (5) GelMA LC. We profiled these organoids at the earliest stages to understand potential differences in radial glia formation.

2024-07-01 | E-MTAB-14203 | 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