Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The induction of integrin beta3 signaling in hematopoietic stem cells (HSCs)

ABSTRACT: To determine the molecules involved in beta3 integrin signaling in HSCs, we carried out DNA microarray analyses using HSCs stimulated with ligand-mimic antibody for intetegrin beta3 in the presence of stem cell factor(SCF) and/or thrombopoietin (TPO). All experiments were performed in duplicate or triplicate using sorted cells that were independently prepared in separate experiments. After CD34-KSL HSCs were cultured with 2C9.G2 or control IgG for 5 days in S-Clone SF-03 medium supplemented with 50 ng/ml SCF and/or 50 ng/ml TPO, gene expression profiles were examimed using 5,000 sorted CD48-KSL cells from each sample.

ORGANISM(S): Mus musculus

SUBMITTER: Terumasa Umemoto

PROVIDER: E-GEOD-33696 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The gene encoding the hematopoietic stem cell regulator CCN3 (NOV) is under direct cytokine control through the transcription factors STAT5a/b.

Project description:Cytokines control the biology of hematopoietic stem and progenitor cells in part through the transcription factors STAT5a/b. CCN3/NOV has been reported as a positive regulator of hematopoietic stem and progenitor cells. We report microarray analyses of Lineage- Sca-1+ c-Kit+ (KSL) cells in the presence and absence of STAT5a/b. Expression of the ccn3 gene was induced over 100-fold in control, but not STAT5a/b-null cells, upon stimulation with a cocktail containing IL-3, IL-6, SCF, TPO and Flt3 ligand. Among the cytokines, IL-3 elevated ccn3 mRNA level in Lineage- c-Kit+ (KL) cells and 32D cells. ChIP assays using 32D cells revealed IL-3-induced binding of STAT5a/b to a GAS site in the ccn3 gene promoter. This is the first report to link two molecules with importance in the regulation of HSCs, CCN3 and STAT5a/b. We report that the regulation and expression of the ccn3 gene is directly controlled by IL-3 through the transcription factors STAT5a/b. Six Control and Six Stat5a/b-null KSL cells, including three biological replications, were unstimulated or stimulated with a cocktail containing IL-3, IL-6, SCF, TPO and FL.

2010-08-25 | E-GEOD-20684 | biostudies-arrayexpress

The induction of integrin beta3 signaling in hematopoietic stem cells (HSCs)

Project description:To determine the molecules involved in beta3 integrin signaling in HSCs, we carried out DNA microarray analyses using HSCs stimulated with ligand-mimic antibody for intetegrin beta3 in the presence of stem cell factor(SCF) and/or thrombopoietin (TPO). All experiments were performed in duplicate or triplicate using sorted cells that were independently prepared in separate experiments.

2011-11-16 | GSE33696 | GEO

global gene expression profiling experiments of HSC cultured in cysteine or valine deficient medium by RNA-sequencing analysis

Project description:We investigated the role of amino acid to maintain HSC function. To identify essential amino acids for HSCs, CD34-KSL cells were cultured in single amino acids deficient medium. And cultured cells were transplanted into lethally irradiated mice. Then, the donor chimerism and lineage contribution was estimated. Surprisingly, HSC proliferation was prevented in valine and cysteine deficient medium in vitro. Donor cells cultured in these medium were also not engrafted. To elucidate the effects and influences of cysteine and valine in HSCs, we performed global gene expression profiling experiments by RNA-sequencing analysis. Gene sets categorized with cell cycle, mitosis, cell division or DNA replication were strongly down-regulated in both valine- or cysteine-depleted conditions These results imply distinctive amino-acid metabolism involved in HSC division. Gene expression profiles of ten thousand HSCs cultured in cysteine or valine deficient medium for 24 hours were compared with that of HSCs cultured in complete medium by using RNA-sequencing analysis

2016-06-26 | E-GEOD-70307 | biostudies-arrayexpress

Expression data 550cGy vs 0cGy KSL

Project description:Precise study of HSCs during regeneration has been impeded by the rarity of the HSC population and depletion of phenotypic HSCs early following genotoxic stresses, such as total body irradiation (TBI). We isolated bone marrow (BM) ckit+sca-1+lin- (KSL) cells, which are enriched for HSCs, from adult C57Bl6 mice before and at several time points following TBI, as a means to map the dynamic molecular response of HSC regeneration. We isolated BM KSL cells and myeloid progenitor cells (c-kit+sca-1-lin- cells) at day +14 after irradiation and compared the gene expression profile of regenerating HSCs versus steady state HSCs (non-irradiated) and committed progenitor cells.

2016-04-05 | E-GEOD-79744 | biostudies-arrayexpress

Role of de novo DNA methyltransferases in hematopoietic stem cells (RNA-seq)

Project description:To investigate the global transcriptome expression in Dnmt3ab dKO HSCs, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified HSCs (SP-KSL-CD150+). With biological duplicates, more than 200 million reads in total for each genotype of HSC were obtained. Mouse hematopoietic stem cell mRNA profiles of Dnmt3ab Dko HSCs, generated by deep sequencing, in duplicate, using Illumina Hiseq 2000

2014-08-19 | E-GEOD-50775 | biostudies-arrayexpress

Identification of the chemokine CCL28 as a growth and survival factor for human hematopoietic stem- and progenitor cells

Project description:To discover novel growth factors for hematopoietic stem- and progenitor cells (HSPCs), we have assessed cytokine responses of cord blood (CB)-derived CD34+ cells in a high-content growth factor screen. We identify the immunoregulatory chemokine (C-C motif) ligand 28 (CCL28) as a novel growth factor that directly stimulates proliferation of primitive hematopoietic cells from different ontogenetic origins. Microarrays are used to compare the expression profiles of HSPCs expanded in SCF, TPO and CCL28 respectively. HSPCs were cultured in Serum-Free Expansion Medium with SCF, SCF + TPO, and SCF + CCL28 respectively, and hybridised microarrays in triplicate.

2013-06-03 | E-GEOD-45136 | biostudies-arrayexpress

Single cell RNA-Seq of mouse bone marrow-derived hematopoietic stem cells after 7-days in viro culture

Project description:Hematopoietic stem cells (HSCs) are cells able to self-renew and differentiate into all blood lineages. We previously have performed serum-free single-cell culture for HSC1 (CD201+CD150+CD48-CD41-CD34-LSK) and competitive repopulation with cultured cells. Single highly purified HSC1 were cultured with stem cell factor (SCF), SCF + G-CSF, or SCF + thrombopoietin (TPO) for 7 days. SCF directly acted on HSC1 and maintained their long-term multilineage reconstitution after serial transplantation. Compared with SCF alone, SCF+G-CSF neither enhanced the number of divisions of HSC1 nor enhanced their levels of reconstitution after serial transplantation. SCF+TPO significantly increased the number of divisions of HSC1. The levels of reconstitution of each lineage in SCF + TPO culture were significantly increased at early months after primary transplantation, however, it gradually decreased after secondary transplantation. Therefore, we performed single-cell RNA-Seq to examine the gene expression of cells cultured with different cytokine combinations.

2023-06-28 | GSE153430 | GEO

Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a [RNA-Seq]

Project description:To investigate the global transcriptome expression in Wild Type mouse hematopoietic stem cells, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified HSCs (SP-KSL-CD150+). With biological duplicates, more than 200 million reads in total were obtained. Mouse hematopoietic stem cell mRNA profiles of wild type mice were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000.

2013-11-16 | E-GEOD-49715 | biostudies-arrayexpress

Transcription profiling of mouse HSC(CD34-KSL cells) and progenitors (CD34+KSL cells)

Project description:Gene expression profile between HSC(CD34-KSL cells) and Progenitors(CD34+KSL cells) were compared.

2010-06-18 | E-MEXP-2223 | biostudies-arrayexpress

Microarray of Human primary megakaryocyte from CALR mutated patient

Project description:CD34+ cells from 5 healthy donors versus 4 essential thrombocythemia patients with CALRm (2 with type 1 (del46 and del52) and 2 with type 2 (del13 and del19)) were in vitro cultured in SCF+TPO condition to enable megakaryocytic differentiation. MK were sorted and RNA were submitted to transcriptomic analysis using gene arrays.

2020-07-01 | E-MTAB-9048 | biostudies-arrayexpress

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