GEO DataSets

(Submitter supplied) Hematopoietic stem cells (HSCs) maintain the entire blood system throughout the life and are utilized for a therapeutic component of blood diseases. The zebrafish is an elegant genetic model for the study of hematopoiesis due to its many unique advantages. We have developed the method to isolate zebrafish HSCs by a combination of two HSC-related transgenic lines, gata2a:GFP and runx1:mCherry. In this study, we performed RNA-seq analysis in three distinct hematopoietic cell populations in the adult kidney, gata2a+ runx1+ cells (HSCs), gata2a− runx1+ cells (erythroid- and/or myeloid-primed progenitors), and gata2a+ runx1− cells (lymphoid-primed progenitors).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

3 Samples

Download data: TXT

(Submitter supplied) Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

5 Samples

Download data: TXT

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

Organism:

Mus musculus; Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL25922 GPL18413

26 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Here we used RNA sequencing to characterize the transcriptional profile of the total RNA from c-Kit+ cells of Runx1 KO and control mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) We used single cell-RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1-mutant cd41-GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic (2.5 days post fertilization, dpf) and larval stages (6, 10 16 dpf).

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25922

9 Samples

Download data: MTX, TSV

(Submitter supplied) Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

6 Samples

Download data: TXT

(Submitter supplied) The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover, transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney, termed the "kidney marrow", providing an attractive tool for studying hematopoietic niches. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

12 Samples

Download data: TXT

(Submitter supplied) Single cell RNA-Seq time-course analysis revealed that as pre-HSCs mature into fetal liver-stage HSCs they show signs of interferon exposure, multi-lineage differentiation gene expression signatures, and prolonged cell cycle reminiscent of quiescent adult HSCs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

127 Samples

Download data: CSV

(Submitter supplied) The goal of this study is to analyse the open chromatin regions via ATACseq in zebrafish embryonic endothelial cells at 26-27hpf using Tg(Kdrl:GFP) transgenic zebrafish embryos. 40000-50000 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

7 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

120 Samples

Download data: BW, MTX, TSV, TXT

(Submitter supplied) RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). We aim to study the role of RUNX1 in megakaryocyte-biased HSCs differentiation to megakaryocytes. Here, by using Runx1F/FMx1-Cre mouse model ,we sorted CD41pos HSCs and CD41neg HSCs in both RUNX1 WT and KO, and tested the RUNX1 direct binding targets in these cells genome.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: BW, TXT

(Submitter supplied) RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). We aim to study the role of RUNX1 in megakaryocyte-biased HSCs differentiation to megakaryocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

90 Samples

Download data: BW, TXT

(Submitter supplied) RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). We aim to study the role of RUNX1 in megakaryocyte-biased HSCs differentiation to megakaryocytes. Here, by using Runx1F/FMx1-Cre mouse model, we sorted CD41pos HSCs and CD41neg HSCs in both RUNX1 WT and KO, and compared their gene expression profiles.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: BW, TXT

(Submitter supplied) RUNX1 is crucial for multiple stages of hematopoiesis and its mutation can cause familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML). We aim to study the role of RUNX1 in megakaryocyte-biased HSCs differentiation to megakaryocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: MTX, TSV

(Submitter supplied) The WT and Tg(RE:HSE:EGFP) F2 generation embryos were heated shocked at 38°C for 1 hour at 16 hpf, then raised to 3 dpf. Total RNAs were isolated with Trizol (Invitrogen). The samples were processed and subsequently analyzed in triplicate on Zebrafish Oligo Microarrays (Agilent Technologies Italia, Italy) which contain 43,554 sets of probes. The microarrays were scanned in an Agilent DNA Microarray Scanner and the images were processed using Feature Extraction software to identify changes of gene expression signatures in Tg(RE:HSE:EGFP) zebrafish embryos.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL21132

2 Samples

Download data: TXT

(Submitter supplied) The global gene expression profiles of human umbilical cord blood and adult bone marrow CD34+CD33-CD38-Rho(lo)c-kit+ cells, enriched for hematopoietic stem/progenitor cells (HSC) with CD34+CD33-CD38-Rho(hi) cells, enriched in committed hematopoietic progenitor cells (HPC), were compared to identify candidate regulators of HSC self-renewal versus differentiation fate decisions. Keywords: parallel sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS1230 GDS1231

Platforms:

GPL96 GPL97

36 Samples

Download data: CEL, EXP

Comparison of CD34+CD33-CD38-Rho(lo)c-kit+ cells, enriched for hematopoietic stem/progenitor cells (HSC), to CD34+CD33-CD38-Rho(hi) cells, enriched for committed hematopoietic progenitor cells (HPC). Cells obtained from umbilical cord blood and bone marrow. Provides insight into control of HSC fate.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 cell type, 2 tissue sets

Platform:

GPL97

Series:

GSE2666

18 Samples

Download data: CEL, EXP

Comparison of CD34+CD33-CD38-Rho(lo)c-kit+ cells, enriched for hematopoietic stem/progenitor cells (HSC), to CD34+CD33-CD38-Rho(hi) cells, enriched for committed hematopoietic progenitor cells (HPC). Cells obtained from umbilical cord blood and bone marrow. Provides insight into control of HSC fate.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 cell type, 2 tissue sets

Platform:

GPL96

Series:

GSE2666

18 Samples

Download data: CEL, EXP

(Submitter supplied) The transcription factor Runx1 is essential for the establishment of definitive hematopoiesis during embryonic development. In adult blood homeostasis, Runx1 plays a pivotal role in the maturation of lymphocytes and megakaryocytes. Furthermore, Runx1 is required for the regulation of hematopoietic stem and progenitor cell (HSPC) pools. However, how Runx1 orchestrates self-renewal and lineage choices in combination with other factors is not well understood. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

8 Samples

Download data: TXT

(Submitter supplied) Ectopic expression of homeodomain transcription factor HoxB4 in mouse ES cells enhances in vitro development of hematopoietic stem cells (HSCs).

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by array

Platforms:

GPL6246 GPL4129 GPL4128

8 Samples

Download data: CEL, TXT