GEO DataSets

(Submitter supplied) Purpose: The histone H3 lysine 36 methyltransferase SETD2 is frequently mutated in various cancers, including leukemia. However, there has not been any functional model to show the contribution of SETD2 in hematopoiesis or the causal role of SETD2 mutation in tumorigenesis. In this study, using a conditional Setd2 knock-out (KO) mouse model, we show that Setd2 deficiency skews hematopoietic differentiation and impaired HSC (hematopoietic stem cell) self-renewal. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

6 Samples

Download data: BW, TXT

(Submitter supplied) Setd2, the histone H3 lysine 36 methyltransferase, plays an important role in the pathogenesis of hematologic malignancies. The research on the role of Setd2 in leukemogenesis has made great progress, but its role in MDS is still unknown. Here, we knock out Setd2 in the NUP98-HOXD13 transgenic (NHD13 Tg) mouse, and demonstrate that loss of Setd2 accelerates the transformation of MDS into AML. The conditional deletion of Setd2 also interferes the differentiation of hematopoietic stem and progenitor cells (HSPCs), and results in the decrease of granulocyte monocyte progenitor (GMP) cells, increase of megakaryocyte erythroid progenitor (MEP) cells and common myeloid progenitor (CMP) cells. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21273 GPL17021

18 Samples

Download data: BED, BROADPEAK, BW, COV, TXT, XLSX

(Submitter supplied) SET domain containing 2 (Setd2), encoding a histone methyltransferase, is associated with many hematopoietic diseases when mutated. By generating a novel exon 6 conditional knockout mouse model, we described an essential role of Setd2 in maintaining the adult hematopoietic stem cells. Loss of Setd2 results in leukopenia, anemia, and increased platelet accompanied with hypocellularity, erythroid dysplasia, and mild fibrosis in bone marrow. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 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

Platforms:

GPL21103 GPL19057

7 Samples

Download data: BEDGRAPH, BW, TXT

(Submitter supplied) Setd2 catalyzes trimethylation of lysine 36 on histone H3. H3K36me3 is deposited mainly in the gene body and has recently been demonstrated to play a role in regulating transcriptional elongation and alternative splicing. We conduct deep sequencing in 2-month old control (APCmin) and APCmin; Setd2IEC-/- mice intestinal cells to understand the splicing events regulated by Setd2.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: BEDGRAPH

(Submitter supplied) Setd2 catalyzes trimethylation of lysine 36 on histone H3. We conduct ChIP sequencing in chromatin landscape induced by Setd2 depleted in mouse intestinal cells to understand the H3K36me3 genome-wide alterations.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BW

(Submitter supplied) We conduct transcriptome comparison of APCmin and APCmin; Setd2IEC-/- mice intestine to gain genomic insights on the biological processes that Setd2 is involved in colon cancer cells. More than 3000 known genes were found changed in the Setd2 depleted cells. Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA) show that the prominent altered pathways in the Setd2 depleted cells are related to Wnt signaling pathway and cell stemness.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: TXT

(Submitter supplied) In this study, we have used inducible and tissue-specific genetic deletion to investigate the function of HBO1 in the hematopoietic system. RNA-seq was used to examine the dependence of gene expression on the presence of HBO1(KAT7). Two different conditional expression sytems were used to induce Cre recombinase and delete a floxed allele of HBO1 in this study. This was to control for the treatement effect during Cre induction (interferon induction of Mx1-cre vs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

32 Samples

Download data: TXT

(Submitter supplied) KAT7 (HBO1) is a histone acetyltransferase required for histone H3 lysine 14 acetylation (H3K14ac) and normal levels of gene expression in hematopoietic stem and progenitor cells (HSPCs). The loss of H3K14ac was detected by western blot in whole bone marrow and by flow cytometry in specific HSPC populations. In order to determine the normal distribution of H3K14ac in the HSPC population a CUT&Tag experiment was performed using lineage negative, cKit positive Sca1 positive cells (LSK) and lineage negative, cKit positive Sca1 negative cells (progenitor cells). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

5 Samples

Download data: TXT

(Submitter supplied) The Hematopoietically-expressed homeobox transcription factor (Hhex) is important for the maturation of definitive hematopoietic progenitors and B-cells during development. We have recently shown that in adult hematopoiesis, Hhex is dispensable for maintenance of hematopoietic stem cells (HSCs) and myeloid lineages but essential for the commitment of Common Lymphoid Progenitors (CLPs) to lymphoid lineages. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Spermatogenesis is precisely cotrolled by complex gene expression programs and involves epigenetic reprogramming including histone modification and DNA methylation. Setd2 catalyzes the trimethylation of histone H3 Lys36 (H3K36me3) and plays key roles in embryonic stem cell differentiation and somatic cell development; however, its role in male germ cell development remains elusive. Here we demonstrate an essential role of Setd2 for spermiogenesis. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21273 GPL17021

14 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Plant homeodomain finger gene 6 (PHF6) encodes a 365-amino-acid protein containing two plant homology domain fingers. Germline mutations of human PHF6 cause Börjeson–Forssman–Lehmann syndrome, a congenital neurodevelopmental disorder. Loss-of-function mutations of PHF6 are detected in patients with acute leukemia, mainly of T cell lineage and in a small proportion of myeloid lineage. The functions of PHF6 in physiological hematopoiesis and leukemogenesis remain incompletely defined. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

21 Samples

Download data: TXT

(Submitter supplied) How specific genetic lesions contribute to transformation of non-malignant myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS) to secondary acute myeloid leukemia (sAML) are poorly understood. The JARID2 gene is lost by chromosomal deletions in a proportion of MPN/MDS patients who progress to sAML. In this study, genetic mouse models and patient-derived xenografts (PDX) demonstrated that Jarid2 acts as a tumor suppressor in chronic myeloid disorders. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21493

32 Samples

Download data: BW, TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL18573 GPL19057

27 Samples

Download data: BW

(Submitter supplied) RNA-seq analysis were performed with total RNA extracted from wt and YTHDF2 KD human UCB CD34+ cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) We performed m6A-seq analysis with sorted mouse LT-HSC, ST-HSC and MPPs.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: BW

(Submitter supplied) We performed m6A-seq analysis with CD34+ human umblilical cord blood HSPCs

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: BW

(Submitter supplied) We performed irCLIP-seq to determine the mRNA targets of YTHDF2 in mouse hematopoietic progenitor cell line HPC-7

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

3 Samples

Download data: BW

(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; Methylation profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

5 Samples

Download data: BED, BW

(Submitter supplied) Recent epidemiological studies have shown that cancer-associated DNMT3A mutations can be detected in the blood of a large proportion of asymptotic elderly individuals. It is important to understand how these mutations provide a competitive advantage to HSCs and allow them to establish clonal dominance. Here we demonstrate that the stress of serial HSC transplantation immortalizes Dnmt3a-null HSCs.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: BED