Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differentially expressed (DE) genes analysis in synovial fluid mesenchymal stem cells (SF-MSCs), SF-MSC derived iPSCs and iPSC derived MSCs (iPSC-MSCs)

ABSTRACT: Differentially expressed (DE) genes analysis in synovial fluid mesenchymal stem cells (SF-MSCs), SF-MSC derived iPSCs and iPSC derived MSCs (iPSC-MSCs)

PROVIDER: PRJNA494570 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7961400.fastq.gz	Fastqsanger.gz
	SRR7961401.fastq.gz	Fastqsanger.gz
	SRR7961393.fastq.gz	Fastqsanger.gz
	SRR7961394.fastq.gz	Fastqsanger.gz
	SRR7961395.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

Differentially expressed (DE) genes analysis in synovial fluid mesenchymal stem cells (SF-MSCs), SF-MSC derived iPSCs and iPSC derived MSCs (iPSC-MSCs)

Project description:We report the application of next-generation sequencing (NGS) to analysis the gene expression profile among three different cells:SF-MSCs, iPSCs and iPSC-MSCs. Our results shown that iPSC-MSCs were more similar to SF-MSCs than iPSCs.

2018-10-04 | GSE120800 | GEO

Murine MSCs: MSC-exosome-hypoxia vs MSC-exosome-normoxia

Project description:Murine MSCs: MSC-exosome-hypoxia vs MSC-exosome-normoxia

| PRJNA490327 | ENA

Proteomic analysis of small extracellular vesicles derived from human iPSC-MSCs

Project description:Human mesenchymal stem cell-derived small extracellular vesicles(MSC-sEVs) have exhibited immunomodulatory and pro-regenerative properties. However, the absence of quantifiable and specific markers for defining and qualifying human MSC-sEVs impedes their translation into clinical practice. Here, we ranked the relative abundances of proteins representing unique signature for MSCs in the proteomic datasets of MSC-sEVs and chose several proteins with high relative abundances as candidate markers for MSC-sEVs. This work would facilitate the establishment of quantifiable, reproducible and standardized assays for defining MSC-sEV preparations, ultimately accelerating the translation of MSC-sEVs into clinical practice.

2024-07-25 | PXD054232 |

Transcriptional Profiling of Werner Syndrome (WS) iPSC-derived MSC and the isogenic gene-edited controls

Project description:WS iPSC (iWS780) is a WRN-null iPSC line derived from AG00780 fibroblast. This iPSC line showed normal 46,XY karyotype. iWS780 was gene-edited by CRIPSR/Cas9 to correct the WRN point mutation. Two clones (C21 & C24) were characterized and showed expression of wild-type WRN protein after gene editing. The iPSC lines (isogenic) were subsequently differentiated into mesenchymal stem cells (MSC). RNA-seq was performed on these MSC.

2019-09-24 | GSE137856 | GEO

RNA-seq analysis of HD and MDS MSCs and MSC-conditioned monocytes

Project description:Altered bone marrow hematopoiesis and immune suppression is a hallmark of myelodysplastic syndrome (MDS). While the bone marrow microenvironment influences malignant hematopoiesis, the mechanism leading to MDS-associated immune suppression is unknown. We tested whether mesenchymal stromal cells (MSCs) contribute to this process. Here, we developed a model to study cultured MSCs from MDS patients compared to similar aged matched normal controls for regulation of immune function. MSCs from MDS patients (MDS-MSC) and healthy donor MSC (HD-MSC) exhibited a similar in vitro phenotype and neither had a direct effect on NK cell function. However, when MDS and HD-MSCs were cultured with monocytes, only the MDS-MSCs acquired phenotypic and metabolic properties of myeloid-derived suppressor cells (MDSCs), with resulting suppression of NK cell function, along with T cell proliferation. A unique MSC transcriptome was observed in MDS-MSCs compared to HD-MSCs, including increased expression of the reactive oxygen species (ROS) regulator, ENC1. High ENC1 expression in MDS-MSC induced suppressive monocytes with increased INHBA, a gene that encodes for a member of the TGF? superfamily of proteins. These monocytes also had reduced expression of the TGF? transcriptional repressor MAB21L2, further adding to their immune suppressive function. Silencing ENC1 or inhibiting ROS production in MDS-MSCs abrogated the suppressive function of MDS-MSC conditioned monocytes. In addition, silencing MAB21L2 in healthy MSC conditioned monocytes mimicked the MDS-MSC suppressive transformation of monocytes. Our data demonstrate that MDS-MSCs are responsible for inducing an immune suppressive microenvironment in MDS through an indirect mechanism involving monocytes.

2020-02-11 | GSE140101 | GEO

Global gene expression (transcriptome) analysis by mRNAseq on iPSC-derived MSCs

Project description:Global gene expression (transcriptome) analysis was performed by messenger RNA sequencing (mRNAseq) on iPSC-derived MSCs produced in three separate lots to determine consistency in gene expression between lots.

2020-07-08 | GSE150969 | GEO

Proteomic analysis of hBM-MSCs and hBM-MSC-derived EVs following lipid perturbations with exogenous sphingomyelinase

Project description:This experiment describes the protomic profiling of human bone marrow-dervied Mesenchymal Stromal Cells and their derived extracellular vesicles following an exogenous treatment of MSCs with neutral sphingomyelinase. Samples were ran in triplicate biological replicates with 1 MSC donor. EV samples were processed using TMTpro 16 plex labeling kit. Samples were injected and measured using a Q exactive Plus high-reslution tandem mass spectrometer.

2025-09-05 | PXD068127 | Pride

Comparison of mesenchymal stem/stromal cells (MSCs) between human iPS-derived MSC and human primary cultured MSCs

Project description:Comparison of mesenchymal stem/stromal cells (MSCs) between human iPS-derived MSC and human primary cultured MSCs

| PRJNA849564 | ENA

Global gene expression (transcriptome) analysis by mRNAseq on iPSC-derived MSCs

Project description:Global gene expression (transcriptome) analysis by mRNAseq on iPSC-derived MSCs

| PRJNA634256 | ENA

Quantitative proteomic analysis of MSC and electrically stimulated MSC (epMSC) secretomes

Project description:This study aimed to investigate the effects of electrical stimulation (ES) on the secretome of mesenchymal stem cells (MSCs). Using quantitative proteomics, we identified a total of 435 proteins secreted by MSCs and ES-treated MSCs (epMSCs), among which 418 were common between groups, with 14 and 8 unique to the epMSC and MSC groups, respectively. Differential expression analysis revealed that 42 proteins were upregulated and 49 were downregulated in the epMSC secretome. Functional enrichment analyses indicated that ES enhances the pro-angiogenic properties of MSCs by modulating pathways such as VEGFA-VEGFR2 signaling and the complement cascade. These findings provide insight into how ES alters MSC-derived secretomes to promote vascularization, which may have therapeutic relevance in regenerative medicine.

2025-09-22 | PXD066035 | Pride

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