GEO DataSets

(Submitter supplied) RNA isolated from sorted cells from zebrafish CHT using HiSeq4000 (Illumina) in paired-read mode.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

4 Samples

Download data: XLS

(Submitter supplied) To profile the developmental landscape of fetal HSPCs and their local niche, here, by using single-cell RNA-sequencing, we decoded the expanding hematopoietic organ in zebrafish

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL23085

2 Samples

Download data: TXT

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

Organism:

Danio rerio

Type:

Expression profiling by array

Platforms:

GPL18413 GPL23085 GPL21741

97 Samples

Download data: TXT

(Submitter supplied) To characterize the distinct features of HSPCs and relevant niche cells, we performed RNA-seq with sorted zebrafish HSPCs and niche cells, based on fluorescent protein labeling from distinct regions at six relatively discrete stages.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21741

24 Samples

Download data: TXT

(Submitter supplied) To decode the complexed mechanism controlling HSC expansion, from the viewpoint of systems biology, we performed spatial transcriptome analysis by dissecting the whole hematopoietic organ, CHT.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

72 Samples

Download data: TXT

(Submitter supplied) To investigate the peculiarity of CHT HSPCs, as well as the interaction of CHT niche and HSPCs at higher resolution, we performed scRNA-seq with zebrafish CHT.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

1 Sample

Download data: TXT

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

Organism:

Danio rerio; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18413 GPL16791

6 Samples

Download data

(Submitter supplied) The microenvironment is an important regulator of hematopoietic stem and progenitor cell (HSPC) biology. Interactions between the niche and stem cells have been difficult to track, but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue (CHT) of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

4 Samples

Download data: XLSX

(Submitter supplied) The microenvironment is an important regulator of hematopoietic stem and progenitor cell (HSPC) biology. Interactions between the niche and stem cells have been difficult to track, but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue (CHT) of the developing zebrafish. Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: XLSX

(Submitter supplied) The zebrafish is a powerful model for the study of hematopoietic stem and progenitor cells (HSPC). We have developed a novel HSPC-specific transgenic line (Runx1+23:GFP). We have used this line in time-lapse live imaging studies to track the migration of HSPC during development. We have also performed a chemical genetic screen to find small molecules that modulate HSPC numbers during development. Treating embryos from 2-3 days post fertilization (2-3 dpf) then fixing for in situ staining with HSPC probes cmyb and runx1, we found the compound lycorine increased HSPC numbers. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL16933

18 Samples

Download data: CEL

(Submitter supplied) We report gene expression data for FACS sorted zebrafish mpeg1:mCherry + and mpx:EGFP + cells collected from whole embryos at 72 hours post fertilization (hpf). We also report gene expression data for the remaining, transgene negative, portion of these embryos.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

3 Samples

Download data: TXT

(Submitter supplied) Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock-down embryos.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

2 Samples

Download data: H5

(Submitter supplied) To better understand molecular phenotypes of Gabbr1 null mutant hematopoietic stem and progenitor cells (HSPCs), we sorted and pooled ~12,000 HSPCs (LSK population) from WT or Gabbr1 null P15 bone marrow for bulk RNA-seq analysis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: TXT

(Submitter supplied) ANGPTL2 is a protein in the angiopoietin-like protein family and plays a role in hematopoietic and vascular physiology. This study examined the effects of ANGPTL2 on CD34+ human hematopoetic progenitor cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

2 Samples

Download data: WIG

(Submitter supplied) ANGPTL2 is a protein in the angiopoietin-like protein family and plays a role in hematopoietic and vascular physiology. This study examined the effects of ANGPTL2 on CD34+ human hematopoetic progenitor cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

6 Samples

Download data: CEL

(Submitter supplied) We report transcriptional heterogeneity of venous endothelial cells (ECs) in the tail of zebrafish embryos, which consist of HSPC-niche-constituting ECs and caudal vessel (CV)-constituting ECs. To characterize isl1-derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue (CHT), we performed single cell RNA sequencing (scRNA-seq) of isl1-derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

2 Samples

Download data: MTX, TSV

(Submitter supplied) Multiple signaling pathways contribute to blood cell formation in the fetus, but a role for innate immune/inflammatory signaling has not been described. Here we show that mouse fetuses deficient for either interferon gamma 1 (IFNg) or its receptor have decreased numbers of lymphoid progenitors and hematopoietic stem cells (HSCs) in the aorta/gonad/mesonephros region and placenta. The role of IFNg signaling was evolutionarily conserved, as morpholino knockdown of IFNg and its receptor reduced the number of hematopoietic stem and progenitor cells in the dorsal aorta and caudal hematopoietic territory of zebrafish embryos, and rag2 expressing cells in the thymus. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

8 Samples

Download data: TXT

(Submitter supplied) In this study, we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First, we generated a comprehensive DNA methylation landscape of EHT, which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1-deficient embryos, we showed that the decreased DNA methylation blocked HSPC emergence. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL24995

34 Samples

Download data: BED, CSV, TXT

(Submitter supplied) RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 (Illumina) in paired-read mode, creating reads with a length of 101 or 151 bp. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other

Platforms:

GPL23274 GPL18413

18 Samples

Download data: XLS

(Submitter supplied) Hematopoietic stem/progenitor cells (HSPCs) are at the basis of the hematopoietic hierarchy. Their ability to self-renew and differentiate is strictly controlled by molecular signals produced by their surrounding micorenvironments composed of stromal cells. HSPCs first emerge in the AGM (Aorta Gonads Mesonephros) region, amplify in the fetal liver (FL) and are maintained in the adult bone marrow (BM). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

51 Samples

Download data: CEL