Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Alternative platelet differentiation pathways initiated by non-hierarchically related hematopoietic stem cells

ABSTRACT: We performed single cell whole transcriptome (Smart-seq3) analysis of hematopoietic stem and progenitor cells long-term replenished by transplanted single Vwf-tdTomato+ P-HSCs (2290 total cells from 7 reconstituted mice) and Vwf-tdTomato Multi-HSCs (2478 total cells from 8 reconstituted mice), as well as control cells from normal mouse bone marrow.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Axel Winroth

PROVIDER: E-MTAB-13935 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Tissue-specific methylomes reveal epigenetic memory in adult mouse tissue

Project description:Cytosine methylation of DNA is an evolutionarily conserved mechanism from plants to animals with crucial roles in gene regulation. However, the variation between methylomes of normal tissues is largely unexplored. To better understand the epigenetic variation of a normal individual, we profiled DNA methylation using whole genome bisulfite sequencing in 17 tissues isolated from an individual mouse. We observed a unique distribution of CpG methylation for each tissue, which cluster based on cell lineage. Global analysis identified only one-eighth of the genome as tissue-specifically methylated. Remarkably, the vast majority of these regions exhibit hallmarks of cis-regulatory activity. Our results also reveal a novel class of dormant enhancers in adult tissues which retain an epigenetic memory of regulatory elements active during development. Together, these results expand the repertoire of regulatory information encoded within the methylome, and suggest mapping it as an alternative method to identify cell-type specific regulatory elements. whole genome bisulfite sequencing of mouse adult tissue

2013-09-01 | E-GEOD-42836 | biostudies-arrayexpress

Base Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

Project description:The study of 5-hydroxylmethylcytosines (5hmC), the sixth base of the mammalian genome, as an epigenetic mark has been hampered by a lack of method to map it at single-base resolution. Previous affinity purification-based methods could not precisely locate 5hmC nor accurately determine its relative abundance at each modified site. We here present a genome-wide approach for mapping 5hmC at base resolution. Application of this new method to the embryonic stem cells not only confirms widespread distribution of 5hmC in mammalian genome, but also reveals a strong sequence bias and strand asymmetry at sites of 5hmC. Additionally, the relative abundance of 5hmC varies significantly depending on the types of functional sequences, suggesting different mechanisms for 5hmC deposition and maintenance. Furthermore, we observe high levels of 5hmC and reciprocally low levels of 5mC at transcription factor binding sites, revealing a dynamic DNA methylation process at cis-regulatory elements. Base resolution sequencing of 5 hydroxymethylcytosine in human and mouse embryonic stem cells

2012-05-16 | E-GEOD-36173 | biostudies-arrayexpress

5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation

Project description:In mammals, cytosine methylation (5mC) is widely distributed throughout the genome but is notably depleted from active promoters and enhancers. While the role of DNA methylation in promoter silencing has been well documented, the function of this epigenetic mark at enhancers remains unclear. Recent experiments have demonstrated that enhancers are enriched for 5-hydroxymethylcytosine (5hmC), an oxidization product of the Tet family of 5mC dioxygenases and an intermediate of DNA demethylation. These results support the involvement of Tet proteins in the regulation of dynamic DNA methylation at enhancers. By mapping DNA methylation and hydroxymethylation at base resolution, we find that deletion of Tet2 causes extensive loss of 5hmC at enhancers, accompanied by enhancer hypermethylation, reduction of enhancer activity, and delayed gene induction in the early steps of differentiation. Our results reveal that DNA demethylation modulates enhancer activity, and its disruption influences the timing of transcriptome reprogramming during cellular differentiation. We performed traditional bisulfite sequencing, TAB-Seq, RNA-Seq, and ChIP-Seq for 6 histone modifications in two biological replicates of wild-type, Tet1-/-, and Tet2-/- mouse ES cells. We also performed RNA-Seq analysis during a timecourse of differentiation to neural progenitor cells.

2014-09-25 | E-GEOD-48519 | biostudies-arrayexpress

FLT3-ITD mutations and TET2 loss synergistically alter global DNA methylation in AML

Project description:Studies of AML patient samples have shown that specific combinations of AML disease alleles confer an adverse outcome, however, in vivo models do not exist for the majority of common, poor-prognosis genotypes. Here we show that TET2/FLT3 mutations can cooperate to induce AML in vivo using a genetically engineered mouse model, and that this model has a defined stem-cell population with a characteristic transcriptional and epigenetic profile. TET2 and FLT3 mutations cooperate to induce site-specific changes in DNA methylation and gene expression, including at loci that regulate hematopoietic differentiation. We demonstrate that re-expression of genes that are silenced in TET2/FLT3-mutant AML restores normal differentiation, demonstrating that the epigenetic program of TET2/FLT3-mutant AML cells can be reversed in vitro and in vivo. Using ERRBS, we profiled genome-wide DNA methylation patterns of the hematopoietic stem cells (LSK) population in Wide-type, Flt3-IDT, Tet2-/-, and Tet2-/-Flt3-IDT mice, each in triplicates

2015-04-14 | E-GEOD-57114 | biostudies-arrayexpress

A highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations

Project description:Investigations of 5-hydroxymethylcytosine (5hmC) in biologically and clinically samples and models with low cell numbers have been hampered by the low sensitivity and reproducibility using current 5hmC mapping approaches. Here, we develop a selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells (nano-hmC-Seal). Using this technology, we profiled the dynamics of 5hmC across different stages of mouse hematopoietic differentiation. Additionally, applying nano-hmC-Seal to the hematopoietic multipotent progenitor cells in an acute myeloid leukemia (AML) mouse model, we identified leukemia-specific, differentially hydroxymethylated regions that harbor previously reported and as-yet-unidentified functionally relevant factors. The change of 5hmC patterns in AML strongly correlates with the altered gene expression on a global scale. Together, our new approach offers a highly sensitive and robust method to study and detect DNA methylation dynamics from in vivo model and clinical samples. Selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells

2016-09-01 | E-GEOD-77967 | biostudies-arrayexpress

Immediate and long-term effects of low doses of Î³-irradiation on hematopoietic stem cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-02-26 | E-GEOD-66376 | biostudies-arrayexpress

Gene profiling of HSCs in C57BL/6 TEL-SYK BM versus control

Project description:The aim of the study was to analyse gene expression differences in LT and ST HSCs in BM of TEL-SYK transplanted versus control C57BL/6mice

2014-12-31 | E-MTAB-2240 | biostudies-arrayexpress

Long-term effects of low doses of Î³-irradiation on hematopoietic stem cells

Project description:Analysis of highly purified long-term hematopoietic stem cells (LT-HSCs) irradiated at 0Gy, 0.02Gy, 0.1Gy and 0.5Gy six months after transplantation. Results provide insight into the molecular mechanisms underlying multiple aspects of LT-HSCs premature ageing after low doses of Î³-irradiation (0.02Gy). Four samples were analyzed and correlated with the control group (0Gy).

2016-02-26 | E-GEOD-66375 | biostudies-arrayexpress

Pre-leukemic Cebpa mutant myeloid progenitors

Project description:In this study, we use pre-malignant cells from different Cebpa mutant acute myeloid leukemia (AML) models. We have used conditional KO models (CreLoxP) and isolated hematopoietic cells shortly after induction of recombination, in order to look at pre-leukemic cells, which have acquired the first hit, but not yet undergone full malignant transformation. We have sorted granulocyte-macrophage progenitors (GMPs) and the more immature population pre-granulocyte-macrophages (preGMs) from pre-leukemic mice. We analyzed gene-expression profiles in order to find deregulated genes, which make the cells more prone to undergo transformation.

2013-07-08 | E-GEOD-47813 | biostudies-arrayexpress

Chromatin profiling of dendritic cells in healthy and hyperglycaemic mice

Project description:The aim of the experiment was to compare chromatin states between healthy and hyperglycaemic mice. We focused on dendritic cells extracted from the lungs. Nuclei were extracted from 200.000 sorted dendritic cells per sample. H3K27me3 and H3K27ac were then profiled using CUT&RUN protocol.

2023-06-29 | E-MTAB-11390 | 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