GEO DataSets

(Submitter supplied) Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals; however, the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision, its dynamic and role in HSPC development is poorly investigated. Here, we performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24995

3 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals; however, the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision, its dynamic and role in HSPC development is poorly investigated. Here, we performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24995

4 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals; however, the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision, its dynamic and role in HSPC development is poorly investigated. Here, we performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

3 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) 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) Hypercholesterolemia, the driving force of atherosclerosis, accelerates the expansion and mobilization of hematopoietic stem and progenitor cells (HSPCs). The molecular determinants connecting hypercholesterolemia with hematopoiesis are underexplored. Here we report that a novel somite-derived pro-hematopoietic cue, AIBP, orchestrates HSPC emergence from the hemogenic endothelium, a type of specialized endothelium manifesting hematopoietic potential. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: WIG

(Submitter supplied) The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead-box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 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 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) Haematopoietic stem cells (HSCs) have long been the focus of developmental and regenerative studies, yet our understanding of the signalling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the FAcilitates Chromatin Transcription (FACT) complex, is required for HSC formation. Zebrafish supt16h mutants express reduced levels of Notch signalling components, genes essential for HSC development, due to abrogated transcription. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: TXT

(Submitter supplied) Hematopoietic stem cells (HSCs) have long been the focus of developmental and regenerative studies, yet our understanding of the signaling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the FAcilitates Chromatin Transcription (FACT) complex, is required for HSC formation. Zebrafish supt16h mutants express reduced levels of Notch signaling components, genes essential for HSC development, due to abrogated transcription. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

6 Samples

Download data: BEDGRAPH

(Submitter supplied) Chromatin organization and accessibility are fundamental to how genes are transcriptionally controlled. We identify the first vertebrate mutant for supt16h, a component of the FACT (FAcilitates Chromatin Transcription) complex along with Ssrp1 known to reorganize nucleosomes and assist in transcriptional elongation. We demonstrate its importance in hematopoietic stem cell (HSC) specification by regulating the elongation of Notch genes. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

2 Samples

Download data: HTML, XLS, XLSX

(Submitter supplied) Chromatin organization and accessibility are fundamental to how genes are transcriptionally controlled. We identify the first vertebrate mutant for supt16h, a component of the FACT (FAcilitates Chromatin Transcription) complex along with Ssrp1 known to reorganize nucleosomes and assist in transcriptional elongation. We demonstrate its importance in hematopoietic stem cell (HSC) specification by regulating the elongation of Notch genes. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

12 Samples

Download data: BW, XLSX

(Submitter supplied) [PROJECT] After fertilization the embryonic genome is inactive until transcription is initiated during the maternal-zygotic transition (MZT). This universal process coincides with the formation of pluripotent cells, which in mammals can be used to generate embryonic stem (ES) cells. To study the changes in chromatin structure that accompany zygotic genome activation and pluripotency, we mapped the genomic locations of histone H3 modifications before and after MZT in zebrafish embryos. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9970

12 Samples

Download data: PAIR, WIG

(Submitter supplied) The goal of this study is genomic chromatin accessibility of 120 hpf zebrafish livers by ATAC-Seq. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and the DNA methylation profile using reduced representation bisulfite sequencing (RRBS).

Organism:

Danio rerio

Type:

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

Platform:

GPL25922

6 Samples

Download data: BEDGRAPH, BROADPEAK

(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