GEO DataSets

(Submitter supplied) The goal of this study is to analyse the open chromatin regions via ATACseq in different sub-types of the zebrafish embryonic dorsal aorta (DA) at 28-30 hpf using TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. 2000-3000 cells were FAC-sorted directly into 100 µl of 1x HBSS/10 mM HEPES/0.25% BSA buffer for Tagmentation (as described by Buenrostro et al. (2013), Nat. Methods 10, 1213-1218), but with 1.5 µl Tn5 transposase (Illumina) in a 50 µl reaction volume. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20828

16 Samples

Download data: BED, BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21741 GPL20828

37 Samples

Download data: BW

(Submitter supplied) The goal of this study is to perform RNAseq in different sub-types of the zebrafish embryonic dorsal aorta (DA) at 28-30 hpf using TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN, Cat No. 74034). High quality RNA (RIN > 8.0) was sent for RNAseq to the Wellcome Trust Centre for Human Genetics (WTCHG). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

21 Samples

Download data: XLSX

(Submitter supplied) Identification of the regulators that lead to arterial specification with definitive hematopoietic potential should help to design strategies to recapitulate HSC development from human pluripotent stem cells (hPSCs). Here, using ETS1 conditional H1 hESC line, we found that ETS1 induction at the mesodermal stage of differentiation dramatically enhances the arterial specification in hPSC cultures and formation of DLL4+CXCR4+/- arterial HE with lymphoid potential and the capacity to produce red blood cells with high expression of BCL11a and b-globin. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) Recently, we identified and characterized specific endothelial progenitors with varying hemogenic potential during human pluripotent stem cell differentiation. Based on these studies we established a platform on which we can manipulate NOTCH signaling on these subsets to elucidate the specific role of this signaling pathway during hemogenic endothelial specification, endothelial-to-hematopoietic transition, and definitive hematopoietic specification.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

4 Samples

Download data: TXT

(Submitter supplied) Hematopoietic Stem Cells (HSC) are originated during embryonic development from endothelial-like cells located in the ventral side of the dorsal aorta around day E10-12 of murine development. This region is called AGM for Aorta/Gonad/Mesonephros refering to the tissues around the hemogenic aorta. Cells that emerge from the endothelium and show hematopoietic traits can be distinguished by the expression of the c-kit receptor and finally acquire the CD45 marker. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

17 Samples

Download data: CEL

(Submitter supplied) Hematopoietic Stem Cells (HSC) are originated during embryonic development from endothelial-like cells located in the ventral side of the dorsal aorta around day E10-12 of murine development. This region is called AGM for Aorta/Gonad/Mesonephros and refers to the tissues around the hemogenic aorta. Cells that emerge from the endothelium and show hematopoietic traits can be distinguished by the expression of the c-kit receptor and finally acquire the CD45 marker.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

6 Samples

Download data: CEL

(Submitter supplied) During development a specialised subset of endothelial cells, the haemogenic endothelium, undergo an endothelial-to-haematopoietic transition. This process critically involves the transcription factor Runx1. Here we have isolated a specific subpopulation of endothelial cells using a Runx1 enhancer-reporter transgenic mouse line (23GFP). We have compared the gene expression profile of this population to non-23GFP expressing endothelial cells and CD41 expressing haematopoietic progenitor cells to assess whether 23GFP expression marks a biologically distinct subset of endothelium. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

9 Samples

Download data: CEL

(Submitter supplied) MicroRNA expression profiling of human microvascular endothelial cells (HMVECs) treated with either vascular endothelial growth factor (VEGF) only or in combination with the natural angiogenesis inhibitor pigment epithelial-derived factor (PEDF). Originally we were interested in the microRNA-mediated regulation of angiogenesis by the endogenous anti-angiogenic PEDF. To identify the microRNAs involved in PEDF signaling in activated endothelial cells, we compared the levels of microRNAs in non-treated microvascular endothelial cells, cells treated with VEGF, and cells treated with a combination of VEGF and PEDF. more...

Organism:

Homo sapiens; Rattus norvegicus; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL15062

2 Samples

Download data: TXT

(Submitter supplied) The transcription factor RUNX1 is required in the embryo for formation of the adult hematopoietic system. Here we describe the seminal findings that led to the discovery of RUNX1 and of its critical role in blood cell formation in the embryo from hemogenic endothelium. We also present RNA-Seq data demonstrating that hemogenic endothelial cells in different anatomic sites, which produce hematopoietic progenitors with dissimilar differentiation potentials, are molecularly distinct. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

16 Samples

Download data: XLSX

(Submitter supplied) Across species, hematopoietic stem and progenitor cells (HSPCs) arise during embryogenesis from a specialized arterial population, termed hemogenic endothelium. Here, we describe a mechanistic role for the epigenetic regulator, Enhancer of zeste homolog-1 (Ezh1) in vertebrate HSPC production via regulation of hemogenic commitment. Loss of ezh1 in zebrafish embryos favored acquisition of hemogenic (gata2b) and HSPC (runx1) fate at the expense of the arterial program (ephrinb2a, dll4). more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL21626 GPL21103

27 Samples

Download data

(Submitter supplied) To examine the cell and molecular transitions between endothelial (E), hemogenic endothelial (HE), and intra-arterial clusters (IAC) cells, and the heterogeneity of hematopoietic stem and progenitor cells (HSPCs) within the IACs, we profiled ~40,000 cells from the caudal arteries (dorsal aorta, umbilical, vitelline arteries) of embryonic day (E) 9.5 to 11.5 mouse embryos by single-cell RNA sequencing (scRNA-Seq). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL21626

26 Samples

Download data: CSV, TXT

(Submitter supplied) To examine the cell and molecular transitions between endothelial (E), hemogenic endothelial (HE), and intra-arterial clusters (IAC) cells, we profiled ~1700 cells from the caudal arteries (dorsal aorta, umbilical, vitelline) of embryonic day (E) 10.5 mouse embryos by single-cell ATAC sequencing (scATAC-Seq). We found extensive cis--regulatory landscape change during the endothelial to hematopoietic transition (EHT).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

1 Sample

Download data: CSV, TSV, TXT

(Submitter supplied) The molecular mechanisms regulating endothelial to hematopoietic transition (EHT) of hemogenic endothelium (HE) are poorly understood. Here we profile the transcriptional changes resulting from SOX7 overexpression during EHT

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TXT, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6238 GPL4134

24 Samples

Download data: TXT

(Submitter supplied) We used a murine ES cell line in which HoxA3 expression is under control of a tetracycline-responsive element and differentiated these cells as embryoid bodies (EBs). Endothelial (Flk-1 VE-cadherin double positive, FV) and hematopoieitc progenitors (c-Kit CD41 double positive, K41) were isolated from differentiated EBs that had been induced for 6 hours by doxycycline (Dox) treatment.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6238

12 Samples

Download data: TXT

(Submitter supplied) We observe that HoxA3 represses hematopoieis by the repression of several transcription factors including Runx1 and Gata1. Up regulation of either Runx1 or Gata1 in the presence of HoxA3 reverted the hematopoietic repression. We have performed full genome analysis to determine the molecular signature of hematopoietic development in response to upregulation of Runx1 and Gata1.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

12 Samples

Download data: TXT

(Submitter supplied) Cell fate decisions during hematopoiesis are governed by lineage-specific transcription factors, such as RUNX1, SCL/TAL1, FLI1 and C/EBP family members. In order to gain insight about how these transcription factors regulate the activation of hematopoietic genes during embryonic development, we measured the genome-wide dynamics of transcription factor assembly on their target genes during the RUNX1-dependent transition from hemogenic endothelium to hematopoietic progenitors. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

13 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Cell fate decisions during hematopoiesis are governed by lineage-specific transcription factors, such as RUNX1, SCL/TAL1, FLI1 and C/EBP family members. In order to gain insight about how these transcription factors regulate the activation of hematopoietic genes during embryonic development, we measured the genome-wide dynamics of transcription factor assembly on their target genes during the RUNX1-dependent transition from hemogenic endothelium to hematopoietic progenitors. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

8 Samples

Download data: TXT