Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of mouse germline stem (GS), multipotent germline stem (mGS), and embryonic stem (ES) cells.

ABSTRACT: A single spermatogonial stem cell can aquire pluripotentiality but that conversion into a pluripotent cell type is accompanied by loss of spermatogenic potential. We used microarrays to compare the expression profiles among the different stem cell types. Experiment Overall Design: GS, mGS and ES cells were cultured for RNA extraction and hybridization on Affymetrix microarrays. We examined the gene expression profiles of GS and mGS cells to find candidate molecules that are involved in the conversion process of GS into mGS cells.

ORGANISM(S): Mus musculus

SUBMITTER: jiyoung lee

PROVIDER: E-GEOD-10610 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparison of gene expression between Xist KO GS cells and wild type GS

Project description:Comparison of gene expression between Xist KO germ line stem GS cells and wildtype GS cells The gene expression of GS cells derived from postnatal mouse testis was investigated. RNA from Xist KO-, wildtype-GS cells, and ES cells were used for this study. 3 independent samples from each cell line were used.

2013-12-01 | E-GEOD-46589 | biostudies-arrayexpress

Transcription profling of glioblastoma stem-like (GS) cell lines, conventional glioma cell lines and primary tumors

Project description:We compared a large panel of human glioblastoma stem-like (GS) cell lines, corresponding primary tumors and conventional glioma cell lines to identify cell lines that preserve the transcriptome of human glioblastomas most closely, thereby allowing identification of shared therapeutic targets. We used Affymetrix HG-U133 Plus 2.0 microarrays to compare human glioblastoma stem-like (GS) cell lines, corresponding primary tumors and conventional glioma cell lines. We extracted total RNA from 32 conventional glioma cell lines, 12 GS cell lines (8 in two different passages), 7 clonal sublines derived from two GS lines, 12 original tumors, and 4 monolayer cultures established from the same tumors as GS-lines using standard serum conditions.

2011-02-12 | E-GEOD-23806 | biostudies-arrayexpress

Gene expression profiles of induced multipotent germline stem cells and other pluripotent stem cells

Project description:Spermatogonial stem cells (SSCs) have pluripotent potential. However, frequency of pluripotent cell derivation is low and the mechanism of culture-induced reprogramming remains unknown. Here we report that epigenetic instability of germline stem (GS) cells, cultured SSCs, induces pluripotent cell derivation. GS cells undergo DNA demethylation in H19 differentially methylated region under low-density culture. When H19 demethylation was induced by Dnmt1 depletion, they converted into embryonic stem (ES)-like cells. Dnmt1 depletion downregulated Dmrt1 expression, whose depletion also induced pluripotency. Functional screening of Dmrt1 target gene revealed that Dmrt1 depletion upregulates Sox2, the key molecule responsible for generating induced pluripotent stem cells. Although Sox2 transfection upregulated Oct4 and produced pluripotent cells, this conversion was inhibited by Oct1 overexpression, suggesting that the balance of Oct proteins maintains SSC identity. These results suggest that culture-induced reprogramming is caused by unstable DNA methylation, and that Dmrt1-Sox2 cascade is critical for regulating pluripotency in SSCs. Pluripotent stem-like cells were induced from GS cells by down-regulation of Dnmt/Dmrt, or up-regulation of Sox2/Oct4 in combination with p53 knock-down and their total RNA samples were subjected to microarray analysis to compare their gene expression profile with other pluripotent stem cells such as ES cells or iPS cells.

2013-10-21 | E-GEOD-43850 | biostudies-arrayexpress

Expression data from mouse germline stem (GS), multipotent germline stem (mGS), and embryonic stem (ES) cells.

Project description:A single spermatogonial stem cell can aquire pluripotentiality but that conversion into a pluripotent cell type is accompanied by loss of spermatogenic potential. We used microarrays to compare the expression profiles among the different stem cell types. Keywords: cell type comparison

2008-02-23 | GSE10610 | GEO

Comparison of gene expression between Xist KO GS cells and wild type GS

Project description:Comparison of gene expression between Xist KO germ line stem GS cells and wildtype GS cells

2013-12-01 | GSE46589 | GEO

Intestinal gene expression in 10-day Giardia duodenalis GS infected mice

Project description:C57BL/6 mice were infected with the GS strain of G. duodenalis and total RNA prepared from the duodenum on day 10. Age matched controls were compared using Affy chips to determine changes in gene expression induced by infection. The majority of induced transcripts are invlved in antibody production. Genes exhibiting the greatest increase in expression are all mast cell transcripts. This is a 4X4 comparison, 4 infected mice and 4 uninfected mice

2013-10-21 | E-GEOD-23372 | biostudies-arrayexpress

Spatial and temporal development of Müller glial cells in hiPSC-derived retinal organoids facilitating the cell enrichment and transcriptome analysis

Project description:Müller glial cells (MGs) play important roles in human retina during physiological and pathological conditions. However, there are still many obstacles to obtain large numbers of human MGs in vitro so far, which hinder the further study of MGs. Human induced pluripotent stem cells (hiPSCs) have capacity to differentiate into almost all body cells, even develop complex, organized tissues, including retinal organoids (ROs) with all cell subtypes, providing many opportunities in study of retinal development and disorders. This study explored the development of MGs within hiPSC-derived ROs and the approach to isolate and expand these MGs. In ROs, MG precursors expressing SOX9 and Ki67 appeared since differentiation day 60 (D60), while SOX9+ CRALBP+ GS+ and Ki67- mature MGs developed from D150. MGs isolated from ROs aged older than 120 days could be expanded and exhibited a spindle-like morphology under adherent culture conditions. These expanded cells expressed MG specific markers SOX9, vimentin, nestin, CRALBP and GS, and responded to L-glutamate stimuli revealed by whole-cell patch-clamp recordings. They could be passaged several times, yielding large numbers of cells in a short period. In addition, they did not transdifferentiate into other types of retinal cells after subretinal transplantation in NOD/SCID mice. This study firstly clarified the timecourse of human MG development in ROs, and established a simple approach to expand and enrich these cells from ROs, paving the way for downstream investigation and application of human MGs.

2022-06-08 | GSE188698 | GEO

A comparison of GS-5759, a bifunctional Î²2-adrenoceptor agonist and PDE4 inhibitor, and indacaterol and GSK 256066 in combination on gene expression changes in the BEAS-2B human airway epithelial cell line

Project description:GS-5759 is a bifunctional ligand composed of a quinolinone-containing pharmacophore found in several Î²2-adrenoceptor agonists linked covalently to a phosphodiesterase 4 inhibitor (PDE4) related to GSK 256066 by a pent-1-yn-1-ylbenzene spacer. The object of the study was to detemine if gene expression changes induced by GS-5759 were replicated by a Î²2-adrenoceptor agonist (indacaterol; Ind) and a PDE4 inhibitor (GSK 256066; GSK) in combination. Microarray analysis was performed on RNA from BEAS-2B cells treated with GS-5759 and a combination of indacaterol and GSK 256066 to identify differentialy expressed genes. Confluent BEAS-2B cells were treated with vehicle, Ind/GSK or GS-5759 for 1h, 2h, 6h or 18h. Total RNA was extracted, quantified (NanoDrop 2000) and the quality of each sample determined by using the Agilent 2100 Lab-on-a-Chip system before being processed for gene expression chnages by Expression Analysis Inc (Dunham, NC, USA).

2016-07-27 | E-GEOD-84880 | biostudies-arrayexpress

Characterization of the scavenger cell proteome in mouse and rat liver

Project description:The structural-functional organization of ammonia and glutamine metabolism in the liver acinus involves highly specialized hepatocyte subpopulations such as glutamine producing perivenous scavenger cells. However, it is still unclear whether this cell population is homogeneous and involves further subpopulations. This was investigated in the present study by proteome profiling of periportal glutamine synthetase-negative hepatocytes and perivenous glutamine synthetase (GS) expressing scavenger cells isolated from mouse and rat liver. Apart from established markers of GS+ hepatocytes such as glutamate transporter 1 (GLT1), ornithine aminotransferase (OAT) or ammonium transporter Rh type B (RHBG), we identified novel scavenger cell-specific proteins such as the basal transcription factor 3 (BTF3) and the heat-shock protein 25 (HSP25). Interestingly, BTF3 and HSP25 were heterogeneously distributed among GS+ hepatocytes as shown by immunofluorescence analyses in mouse, rat and human liver slices. Feeding experiments showed that RHBG but not GS protein levels were increased in the liver of mice fed with a high protein diet compared to standard chow. While the spatial distribution of GS and carbamoylphosphate synthetase-1 (CPS1) was not affected, periportal areas constituted by GLS2 positive hepatocytes were enlarged or reduced in response to high or low protein diet, respectively. The data suggest that the population of perivenous GS+ scavenger cells is heterogeneous and not uniform as previously suggested which may reflect a functional heterogeneity, possibly relevant for liver regeneration.

2021-08-05 | PXD023561 | Pride

Gene expression profiles of induced multipotent germline stem cells and other pluripotent stem cells

2013-10-21 | GSE43850 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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