GEO DataSets

(Submitter supplied) Purpose: The goals of this study are to determine possible downstream targets of Twist1 in bone marrow stromal cells with or without Twist1 knockout. Methods: gene expression profiling with or without Twist1 knockout in bone marrow stromal cells were generated by deep sequencing, using Illumina Hiseq.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: TXT

(Submitter supplied) The Polymerase Associated Factor 1 complex (PAF1c) functions at the interface of epigenetics and gene transcription and plays a role in solid tumors and leukemia. Previous reports demonstrated that the PAF1c is required for MLL-fusion driven acute myeloid leukemia (AML) through the direct regulation of pro-leukemic target genes like Hoxa9 and Meis1. This is due to direct interactions between the PAF1c and wild type MLL or MLL fusion proteins. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: CSV

(Submitter supplied) We investigated the role of PRMT4 in normal and malignant hematopoiesis. We found that knockdown of PRMT4 impairs cell cycle progression, induces apoptosis, and downgretulateds E2F target genes in leukemia cell lines, identifying several mechanisms for the leukemia-specific dependence on PRMT4.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

27 Samples

Download data: TXT

(Submitter supplied) Signal transducer and activator of transcription 5 (STAT5a and STAT5b) are intrinsically critical for normal hematopoiesis but are also expressed in stromal cells. However, hematopoiesis-supporting stromal function has not been reported. Here, STAT5ab knockout (KO) was generated with a variety of bone marrow hematopoietic and stromal Cre transgenic mouse strains. Pan-hematopoietic deletion with Vav1-Cre was the positive control for loss of multipotent hematopoietic function but surprisingly dysregulated niche factor mRNA expression and deleted STAT5ab in CD45neg cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: MTX, TSV

(Submitter supplied) In an attempt to clarify the diferrence of exosomal microRNA derived from Normal BM and primary AML CD34+ cells. Primary cells were cultured in serum free medium and supernatant was harvested. After extract microRNAs, the difference of exosomal microRNAs between normal BM and leukemia was analyzed by array.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL18941

3 Samples

Download data: TXT

(Submitter supplied) Group 1 -- WT or PRDM16-KO ex vivo murine MLL-AF9 cells, and PRDM16-KO AF9 cells overexpressing either f-PRDM16 or s-PRDM16. Group 2 -- WT or total PRDM16-KO murine HSCs isolated from adult BM. Group 3 -- WT or total PRDM16-KO murine HSCs isolated from fetal liver. Group 4 -- WT or f-PRDM16-KO murine HSCs (expressing s-PRDM16 only) isolated from fetal liver.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

32 Samples

Download data: TXT

(Submitter supplied) Zinc finger protein 521 (ZFP521), a DNA-binding protein containing 30 Krüppel-like zinc fingers, has been implicated in the differentiation of multiple cell types, including hematopoietic stem and progenitor cells (HSPC) and B lymphocytes. Here, we report a novel role for ZFP521 in regulating the earliest stages of hematopoiesis and lymphoid cell development through soluble microenvironmental proteins. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: TXT

(Submitter supplied) Bone marrow (BM) niche contributes to hematopoietic regeneration and can be remodeled by leukemic cells. We have found that Lama4 deletion in mouse mesenchymal stem cells (MSCs) could promote the proliferation of MLL-AF9 acute myeloid leukemia (AML) cells and chemoresistance of the cells to chemotherapy cytarabine. However, whether Lama4 deficient MSCs are more susseptible for AML cell remodeling remains to be explored. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

22 Samples

Download data: XLSX

(Submitter supplied) Bone marrow (BM) niche contributes to hematopoietic regeneration under stress like irradiation and leukemia. However, the mechanisms remain poorly defined. We here report that Lama4 deletion in mice results in reduction of mesenchymal progenitors (MPCs) and endothelial cells in BM. Following irradiation, Lama4-/- mice displayed impaired hematopoiesis recovery accompanied with dysregulation of BM niche factors like angiopoietin-1 and Tgfb1 in the MPCs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

6 Samples

Download data: TXT

(Submitter supplied) Estrogens are potential regulators of the hematopoietic stem cell (HSC) niche and have effects on mature hematopoietic cells; however, whether estrogen signaling directly regulates normal and malignant HSC remains unclear. We demonstrate differential expression and specific roles of estrogen receptors (ER) in hematopoietic progenitors. ERa activation in short-term HSC and multipotent progenitors induced apoptosis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

18 Samples

Download data: TXT

(Submitter supplied) Erg is an ETS family transcription factor frequently overexpressed in human leukemias and has been implicated as a key regulator of hematopoietic stem cells (HSCs). However how Erg controls normal hematopoiesis, particularly at the stem cell level, remains poorly understood. Using homologous recombination, we generated an Erg knockdown allele (Ergkd) in which Erg expression can be restored upon Cre-mediated excision of a Stopper cassette. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Alterations of TWIST-1 expression are often seen in solid tumors and contribute to tumorigenesis and cancer progression. However, studies concerning its pathogenic role in leukemia are scarce. Here we show that TWIST-1 is a new candidate gene contributing to leukemogenesis of myeloid leukemia. We used array as one tool to determine gene expression profiles of control and TWIST-1-overexpressing U937 cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

2 Samples

Download data: CEL

(Submitter supplied) Murine models of myeloid neoplasia show how leukemia infiltration alters the mesenchymal stem and progenitor cells to reinforce malignancy at the expense of healthy hematopoiesis. However, little is known about the bone marrow architecture in humans. We used global gene expression analyses to analyze mesenchymal stem and progenitor cells from AML patients and compared with mesenchymal stem and progenitor cells from the non-leukemic donor.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

11 Samples

Download data: CEL, CHP

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TSV

(Submitter supplied) Chromosomal translocation t(8;21) (q22;q22) leading to generation of oncogenic RUNX1-RUNX1T1 (AML1-ETO) fusion is a cytogenetic abnormality observed in about 10% of acute myelogenous leukemia (AML). To uncover somatic mutations that cooperate with t(8;21)-driven leukemia, we performed targeted and whole exome sequencing of newly-diagnosed and relapsed AML samples. We identified high frequency of truncating alterations in ASXL2 along with recurrent mutations of KIT, TET2, MGA, FLT3, and DHX15 in this subtype of AML. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TSV

(Submitter supplied) Chromosomal translocation t(8;21) (q22;q22) leading to generation of oncogenic RUNX1-RUNX1T1 (AML1-ETO) fusion is a cytogenetic abnormality observed in about 10% of acute myelogenous leukemia (AML). To uncover somatic mutations that cooperate with t(8;21)-driven leukemia, we performed targeted and whole exome sequencing of newly-diagnosed and relapsed AML samples. We identified high frequency of truncating alterations in ASXL2 along with recurrent mutations of KIT, TET2, MGA, FLT3, and DHX15 in this subtype of AML. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

10 Samples

Download data: TSV

(Submitter supplied) To investigate usage of exon 8 in ZNF384 in different myeloid/lymphoid populations from MPAL/BALL PDX and cell lines

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

8 Samples

Download data: TSV

(Submitter supplied) We report changes in chromatin occupancy dependent on TCF3-ZNF384 splicing isoform usage. The isoform including exon 8, which encodes 2 zinc finger domains, has increased binding near genes important for nomal hematopoiesis. We report no global changes in H3K27Ac upon expression of ZNF384 fusions but 47 loci with increased H3K27Ac.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

26 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) RNA-seq of multiple models of ZNF384-rearrangments (transplanted human CD34 cells and transplanted mouse lineage negative cells) to determine differentially expressed genes.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

38 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL24676 GPL24247

81 Samples

Download data: BW, MTX, NARROWPEAK, TSV, TXT