E-GEOD-35561
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA152683
PROVIDER: E-GEOD-35561 | ExpressionAtlas | 2015-09-22
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Expression data from trisomy 21 and euploid induced pluripotent stem cell hematopoietic progenitors
| PRJNA152683 | ENA
Project description:Collombet2016 - Lymphoid and myeloid cell
specification and transdifferentiation
This model is described in the article:
Logical modeling of lymphoid
and myeloid cell specification and transdifferentiation
Samuel Collombet, Chris van Oevelen,
Jose Luis Sardina Ortega, Wassim Abou-Jaoudé, Bruno Di
Stefano, Morgane Thomas-Chollier, Thomas Graf, and Denis
Thieffry
Proceedings of the National Academy of
Sciences of the United States of America
Abstract:
Blood cells are derived from a common set of hematopoietic
stem cells, which differentiate into more specific progenitors
of the myeloid and lymphoid lineages, ultimately leading to
differentiated cells. This developmental process is controlled
by a complex regulatory network involving cytokines and their
receptors, transcription factors, and chromatin remodelers.
Using public data and data from our own molecular genetic
experiments (quantitative PCR, Western blot, EMSA) or
genome-wide assays (RNA-sequencing, ChIP-sequencing), we have
assembled a comprehensive regulatory network encompassing the
main transcription factors and signaling components involved in
myeloid and lymphoid development. Focusing on B-cell and
macrophage development, we defined a qualitative dynamical
model recapitulating cytokine-induced differentiation of common
progenitors, the effect of various reported gene knockdowns,
and the reprogramming of pre-B cells into macrophages induced
by the ectopic expression of specific transcription factors.
The resulting network model can be used as a template for the
integration of new hematopoietic differentiation and
transdifferentiation data to foster our understanding of
lymphoid/myeloid cell-fate decisions.
This model is hosted on
BioModels Database
and identified by:
MODEL1610240000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-06-08 | MODEL1610240000 | BioModels
Project description:Expression data of induced pluripotent stem cell
| PRJNA116495 | ENA
Project description:The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. In contrast, maturation capacity (hematopoietic precursors to mature blood) is affected by iPSC origin; blood-derived iPSCs showed the highest capacity. However, some fibroblast-derived iPSCs showed higher capacity than blood-derived clones. Tracking of DNA methylation changes during reprogramming reveals that maturation capacity is highly associated with aberrant DNA methylation acquired during reprogramming, rather than the types of iPSC origins. These data demonstrated that variations in the hematopoietic differentiation capacity of iPSCs are not attributable to somatic memories of their origins. Methyl-seq analysis for undifferentiated induced pluripotent stem cell (iPSC) lines (n = 21), human dermal fibroblast (HDF, n = 1), human peripheral blood (n = 1), and human keratinocyte (n = 1), and ATAC-seq analysis for 2 iPSC lines and an embryonic stem cell (ESC) line with two different culture conditions. CTCF-ChIP-seq analysis for an ESC line.
2016-07-27 | E-GEOD-74967 | biostudies-arrayexpress
Project description:Single cell RNA-seq study of induced pluripotent stem cell derived neural stem cells. Analysis of gene expression over cell clusters identified inherent presence of neurogenic progenitors and gliogenic progenitors in established neural stem cells. This study aids to explain heterogeneity of neural stem cell identity and resolves gene expression enrichment in subpopulations of diverse progenitors. Processed and quality controlled data sets used for generating figure 4 in published article. Single cell raw data files for experiments were not made available.
2019-10-24 | E-MTAB-8363 | biostudies-arrayexpress
Project description:Single cell RNA-seq study of induced pluripotent stem cell derived neural stem cells. Analysis of gene expression over cell clusters identified inherent presence of neurogenic progenitors and gliogenic progenitors in established neural stem cells. This study aids to explain heterogeneity of neural stem cell identity and resolves gene expression enrichment in subpopulations of diverse progenitors. Processed and quality controlled data sets used for generating figure 2 in published article. Single cell raw data files for experiments are not available for public download.
2019-10-24 | E-MTAB-8379 | biostudies-arrayexpress
Project description:Single cell RNA-seq study of induced pluripotent stem cell derived neural stem cells. Analysis of gene expression over cell clusters identified inherent presence of neurogenic progenitors and gliogenic progenitors in established nerual stem cells. This study aids to explain heterogeneity of neural stem cell identity and resolves gene expression enrichment in subpopulations of diverse progenitors. Processed and quality controlled data sets used for generating figure 3 in published article. Single cell raw data files for experiments are not available for public download.
2019-10-24 | E-MTAB-8383 | biostudies-arrayexpress
Project description:Infections are associated with extensive consumption of blood platelets representing a high risk for health. How the hematopoietic system coordinates the rapid and efficient regeneration of this particular lineage during such stress scenarios remains unclear. Here we report that the phenotypic hematopoietic stem cell (HSC) compartment contains highly potent megakaryocyte-committed progenitors (hipMkPs), a cell population that shares many features with multipotent HSCs and serves as a lineage-restricted emergency pool for inflammatory insults. Our data show that during homeostasis, hipMkPs are maintained in a primed but quiescent state, thus contributing little to steady-state megakaryopoiesis. Moreover, homeostatic hipMkPs show expression of megakaryocyte lineage priming transcripts for which protein synthesis is suppressed. We demonstrate that acute inflammatory signaling instructs activation of hipMkPs, as well as Mk protein production from pre-existing transcripts and drives a rapid maturation of hipMkPs and other Mk progenitors. This results in an efficient regeneration of platelets that are lost during inflammatory insult. Thus, our study reveals an elegant emergency machinery that counteracts life-threating depletions in the platelet pool during acute inflammation.
2015-08-26 | PXD001500 | Pride
Project description:Similar to embryo-derived stem cells, application of human induced pluripotent stem cells (iPSCs) is limited by our understanding of lineage specification. Here, we demonstrate the ability to generate progenitors and mature cells of the hematopoietic fate directly from human dermal fibroblasts without establishing pluripotency. POU domain activation of hematopoietic transcription factors by ectopic expression of Oct-4, together with specific cytokine treatment, allowed generation of cells expressing the pan-leukocyte marker CD45. These unique fibroblast-derived cells gave rise to granulocytic, monocytic, megakaryocytic, and erythroid lineages, and demonstrated in vivo engraftment capacity. Distinct from PSC-derived hematopoietic cells, adult and not embryonic hematopoietic programs are activated, consistent with bypassing pluripotent state to generate blood fate. These findings suggest an alternative approach to cellular reprogramming for autologous cell-replacement therapies that avoids complications associated with the use of human PSCs. Molecular analysis was done on purified untransduced Fibs, Oct-4 transduced Fibs at day 4, CD45+ve Fibs at day 21 and hematopoietic cytokine treated CD45+ve Fibs at day 37. The day 4 Oct-4 transduced Fibs were isolated by puromycin selection overnight (Oct-4 vector contains puromycin resistance cassette), purity of sample was validated by staining for Oct-4 followed by Oct-4 expression analysis using flow cytometry; samples used for molecular analysis exhibited 99% Oct-4 levels. The day 21 and day 37 CD45+veFibsOct-4 were isolated based on their CD45 expression. D21 and D37 cells were stained with CD45-APC antibody (BD Biosciences) and sorted using FACSAria II (Becton- Dickinson); samples used for molecular analysis exhibited 99% CD45 levels. Analysis was performed on two biological replicates per sample.
2010-10-20 | E-GEOD-24621 | biostudies-arrayexpress
Project description:Hamey2017 - Blood stem cell regulatory
network
This model is described in the article:
Reconstructing blood stem
cell regulatory network models from single-cell molecular
profiles
Fiona K. Hamey, Sonia Nestorowa,
Sarah J. Kinston, David G. Kent, Nicola K. Wilson, and Berthold
Göttgens
Proceedings of the National Academy of
Sciences of the United States of America
Abstract:
Adult blood contains a mixture of mature cell types, each
with specialized functions. Single hematopoietic stem cells
(HSCs) have been functionally shown to generate all mature cell
types for the lifetime of the organism. Differentiation of HSCs
toward alternative lineages must be balanced at the population
level by the fate decisions made by individual cells.
Transcription factors play a key role in regulating these
decisions and operate within organized regulatory programs that
can be modeled as transcriptional regulatory networks. As
dysregulation of single HSC fate decisions is linked to fatal
malignancies such as leukemia, it is important to understand
how these decisions are controlled on a cell-by-cell basis.
Here we developed and applied a network inference method,
exploiting the ability to infer dynamic information from
single-cell snapshot expression data based on expression
profiles of 48 genes in 2,167 blood stem and progenitor cells.
This approach allowed us to infer transcriptional regulatory
network models that recapitulated differentiation of HSCs into
progenitor cell types, focusing on trajectories toward
megakaryocyte–erythrocyte progenitors and lymphoid-primed
multipotent progenitors. By comparing these two models, we
identified and subsequently experimentally validated a
difference in the regulation of nuclear factor, erythroid 2
(Nfe2) and core-binding factor, runt domain, alpha subunit 2,
translocated to, 3 homolog (Cbfa2t3h) by the transcription
factor Gata2. Our approach confirms known aspects of
hematopoiesis, provides hypotheses about regulation of HSC
differentiation, and is widely applicable to other hierarchical
biological systems to uncover regulatory relationships.
This model is hosted on
BioModels Database
and identified by:
MODEL1610060000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-06-09 | MODEL1610060000 | BioModels