GEO DataSets

(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) 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:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21741

12 Samples

Download data: BW, XLSX

(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) 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) Hematopoietic stem cells (HSCs) possess the potential for self-renew and the capacity, throughout life, to differentiate into all blood cell lineages. Yet, the mechanistic basis for HSC development remains largely unknown. In this study, we characterized a zebrafish smu471 mutant with hematopoietic stem/progenitor cell (HSPC) defects and found that sart3 was the causative gene. RNA expression profiling of the sart3smu471 mutant revealed spliceosome and p53 signaling pathway to be the most significantly enriched pathways in the sart3smu471 mutant. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: CSV

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

Organism:

Danio rerio

Type:

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

Platforms:

GPL24995 GPL18413

14 Samples

Download data: BW, TXT

(Submitter supplied) The RNA N6-methyladenosine (m6A) modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However, its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells (HSPCs) during early embryonic development remain elusive. Here we show that Mettl16, an RNA methyltransferase identified recently, is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A-dependent manner. In mettl16 deficient embryos, HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. more...

Organism:

Danio rerio

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24995

8 Samples

Download data: BW

(Submitter supplied) The RNA N6-methyladenosine (m6A) modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However, its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells (HSPCs) during early embryonic development remain elusive. Here we show that Mettl16, an RNA methyltransferase identified recently, is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A-dependent manner. In mettl16 deficient embryos, HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

6 Samples

Download data: TXT

(Submitter supplied) Purpose: This study aims to evaluate the effect of FACT complex inhibitor CBL0137 to the total transcriptome of NK-92 cells through RNA-seq assay. Methods: NK-92 cells were treated with CBL0137 (500 nM) or DMSO for 24 h. RNA samples were extracted and submitted to GENEWIZ (South Plainfield, NJ 07080) for quality control and subsequent rRNA removal through polyA selection, followed by the library preparation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

19 Samples

Download data: CEL

(Submitter supplied) Notch signaling is one of the central regulators of differentiation in a variety of organisms and tissue types. Within the hematopoietic system, Notch is essential for the emergence of definitive HSC during fetal life and controls adult HSC differentiation to the T-cell lineage. Notch activation is controlled by the gamma-secretase complex complex, composed of presenilin, nicastrin (Ncstn), anterior pharynx-1 (Aph1), and presenilin enhancer-2 To determine other role of Notch signaling in HSC we designed a conditional mouse model of Nicastrin deletion. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

9 Samples

Download data: CEL

(Submitter supplied) Notch signaling is one of the central regulators of differentiation in a variety of organisms and tissue types. Within the hematopoietic system, Notch is essential for the emergence of definitive HSC during fetal life and controls adult HSC differentiation to the T-cell lineage. Notch activation is controlled by the gamma-secretase complex complex, composed of presenilin, nicastrin (Ncstn), anterior pharynx-1 (Aph1), and presenilin enhancer-2 To determine other role of Notch signaling in HSC we designed a conditional mouse model of Notch activation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Notch signaling is one of the central regulators of differentiation in a variety of organisms and tissue types. Within the hematopoietic system, Notch is essential for the emergence of definitive HSC during fetal life and controls adult HSC differentiation to the T-cell lineage. Notch activation is controlled by the gamma-secretase complex complex, composed of presenilin, nicastrin (Ncstn), anterior pharynx-1 (Aph1), and presenilin enhancer-2 To determine other role of Notch signaling in HSC we designed a conditional mouse model of Nicastrin deletion. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

(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) 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) 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