GEO DataSets

(Submitter supplied) We report the application of H3K27me3 ChI-seq assays in hematopoietic stem and progenitors cells (HSPCs) from p53+/+ and p53R248W/+ mutant mice. We also performed RNA-seq assays to examine the impact of p53 on gene expression in hematopoietic stem and progenitor cells.

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL21103

11 Samples

Download data: BW, TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

64 Samples

Download data: COV

(Submitter supplied) Clonal hematopoiesis (CH) increases risk for the development of hematological malignancy and cardiovascular disease. IL1β is elevated in patients with CH and its inhibition mitigates cardiovascular risk in murine models with Tet2 loss-of-function. How IL1β alters population dynamics of hematopoietic cells upon Tet2 deletion (Tet2-KO) is not well understood. We demonstrated IL1β expands Tet2-KO neutrophils, monocytes/macrophages, and long-term hematopoietic stem cells with reduced lymphopoiesis. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

48 Samples

Download data: COV

(Submitter supplied) Clonal hematopoiesis (CH) increases risk for the development of hematological malignancy and cardiovascular disease. IL1β is elevated in patients with CH and its inhibition mitigates cardiovascular risk in murine models with Tet2 loss-of-function. How IL1β alters population dynamics of hematopoietic cells upon Tet2 deletion (Tet2-KO) is not well understood. We demonstrated IL1β expands Tet2-KO neutrophils, monocytes/macrophages, and long-term hematopoietic stem cells with reduced lymphopoiesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) MYSM1 is a transcriptional regulator essential for HSC function and hematopoiesis. We established that p53 activation is a common mechanism mediating HSC dysfunction, MPP depletion, and lymphopenia in Mysm1-deficiency, however, the specific p53-induced effectors that trigger dysfunction in Mysm1-deficient HSPCs remain unknown. Here, we performed RNA-Seq of Lin-cKit+Sca1+CD150+ and CD150- HSPCs from Mysm1-/-Puma-/-, Mysm1-/-Puma+/-, Puma-/-, and wild-type mice; (Mysm1-/-Puma+/- phenocopies Mysm1-/-). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

29 Samples

Download data: TXT

(Submitter supplied) Next-generation sequencing (NGS) has been used for study the transcriptomic and genomic change after Chd8 dletion. The goals of this study are to compare NGS-derived LSK transcriptome profiling (RNA-seq), ATAC and H3K4me3 and H3K27me3 Cut&Run data to find downstream targets of CHD8 and its impact on chromatin state.

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

22 Samples

Download data: BW, XLS

(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:

GPL17021

16 Samples

Download data: BW, TXT

(Submitter supplied) Stem and progenitor cells are the main mediators of tissue renewal and repair, both under homeostatic conditions and in the response to physiological stress and injury. Hematopoietic system is responsible for the regeneration of blood and immune cells, and is maintained by bone marrow resident hematopoietic stem and progenitor cells (HSPCs). Hematopoietic system is particularly susceptible to injury in response to genotoxic stress, resulting in risk of bone marrow failure and secondary malignancies in cancer patients undergoing radiotherapy. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: BED, BW

(Submitter supplied) Stem and progenitor cells are the main mediators of tissue renewal and repair, both under homeostatic conditions and in the response to physiological stress and injury. Hematopoietic system is responsible for the regeneration of blood and immune cells, and is maintained by bone marrow resident hematopoietic stem and progenitor cells (HSPCs). Hematopoietic system is particularly susceptible to injury in response to genotoxic stress, resulting in risk of bone marrow failure and secondary malignancies in cancer patients undergoing radiotherapy. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) Whole genome expression of bone marrow deived hepatocytes after 1 and 5 months of transplantation are compared with that of primary hepatocytes and Lin- BM cells

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL13381 GPL20964

8 Samples

Download data: 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) In this study, we establish a mechanism in which mutant p53 cooperates with MLL4 to regulate aberrant enhancer activity and tumor promoting gene expression in response to chronic TNF-a signaling.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

5 Samples

Download data: BIGWIG

(Submitter supplied) Genomic sequencing of hepatocellular carcinoma (HCC) uncovers a paucity of actionable mutations, underscoring the necessity to exploit epigenetic vulnerabilities for therapeutics. In HCC, EZH2-mediated H3K27me3 represents a major oncogenic chromatin modification, but how it modulates the therapeutic vulnerability of signaling pathways remains unknown. Here, we identified that EZH2 maintains H3K27 methylome through epigenetic silencing of specific gene sets. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

10 Samples

Download data: BW

(Submitter supplied) The polycomb group (PcG) proteins function in gene silencing through histone modifications. They form chromatin-associated multiprotein complexes, termed polycomb repressive complex (PRC) 1 and PRC2. These two complexes work in a coordinated manner in the maintenance of cellular memories through transcriptional repression of target genes. EZH2 is a catalytic component of PRC2 and trimethylates histone H3 at lysine 27 to transcriptionally repress the target genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

4 Samples

Download data: TXT

(Submitter supplied) Through high-throughput RNA immunoprecipitation sequencing (RIP-seq), we discovered that EZH2 protein associates with messenger RNAs of a number of genes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: BW

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

Organism:

Danio rerio; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24995 GPL24676

12 Samples

Download data

(Submitter supplied) Purpose: To explore the mechanism of how Tan I inhibits malignant hematopoiesis at the gene expression level Methods: 72 hpf Tg(c-mybhyper: GFP) zebrafish embryos treated with DMSO or Tan I 60 μM were collected for RNA sequencing Results: We found that 1882 genes were differentially expressed between DMSO and Tan I treatment in c-mybhyper fish embryos (p value <=0.05, |log2 fold change| >= 0.25) Conclusions: We identified MMP9 and ABCG2 as two possible downstream genes of Tan I’s effects on EZH2

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

6 Samples

Download data: CSV

(Submitter supplied) Purpose: To explore the mechanism of how Tan I inhibits malignant hematopoiesis at the gene expression level Methods: NB4 cells treated with DMSO or Tan I 10 μM were collected for RNA sequencing Results: We found that 376 genes were differentially expressed between DMSO and Tan I treatment in the NB4 cells (p value <=0.05, |log2 fold change| >= 0.25) Conclusions: We identified MMP9 and ABCG2 as two possible downstream genes of Tan I’s effects on EZH2

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

24 Samples

Download data: BIGWIG

(Submitter supplied) With an overall 5%-10% incidence rate in acute myeloid leukemia (AML), the occurrence of TP53 mutations is low compared with that in solid tumors. However, when focusing on high-risk groups including secondary AML (sAML) and therapy-related AMLs, the frequency of mutations reaches up to 35%. Mutations may include loss of heterozygosity (LOH) or deletion of the 17p allele, but are mostly missense substitutions that are located in the DNA-binding domain. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: BIGWIG