GEO DataSets

Analysis of ETV6/RUNX1 (E/R) fusion gene-positive, BCP ALL cell lines (AT2 and REH) following E/R knockdown. E/R (also known as TEL/AML1) is the most frequent gene fusion in childhood ALL. Results provide insight into role of E/R gene fusion in leukemia propagation and maintenance.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 cell line, 2 protocol sets

Platform:

GPL570

Series:

GSE29639

10 Samples

Download data: CEL

(Submitter supplied) Background: ETV6/RUNX1 (E/R) (also known as TEL/AML1) is the most frequent gene fusion in childhood acute lymphoblastic leukemia (ALL) and also most likely the crucial factor for disease initiation, whereas its role in leukemia propagation and maintenance remains largely elusive. To address this issue we performed a shRNA-mediated knock-down (KD) of the E/R fusion gene and investigated the ensuing consequences on genome-wide gene expression patterns and deducible regulatory functions in two E/R-positive leukemic cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4298

Platform:

GPL570

10 Samples

Download data: CEL

(Submitter supplied) The gene expression profile of E/R KO clones versus REH cells and controls clones, analysed by total RNA-sequencing, showed a total of 342 genes differentially expressed (q<0.05), 182 upregulated and 160 downregulated. The heatmap of the top50 of the most deregulated genes according to fold change (FC) values showed a distinct expression signature of E/R KO clones as compared with REH cells and control clones

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: CSV, XLSX

(Submitter supplied) Background The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AML1-positive patients are thus an interesting subgroup to study, and such studies should elucidate the biological processes underlying TEL/AML1 pathogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1708

33 Samples

Download data: TXT

(Submitter supplied) Around 20-25% of childhood acute lymphoblastic leukemias carry the TEL-AML1 (TA) fusion gene. It is a fusion of two central hematopoietic transcription factors, TEL (ETV6) and AML1 (RUNX1). Despite its prevalence, the exact genomic targets of TA have remained elusive. We evaluated gene loci and enhancers targeted by TA genome-wide in precursor B acute leukemia cells using global nuclear run-on sequencing (GRO-seq).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Arrested bone marrow (BM) lymphoid cell differentiation underlies the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). Recurrent genetic lesions often directly involve transcription factors (TFs), such as ETV6 and RUNX1 found in the most common ALL translocation. Here, we studied differential gene expression in ETV6-RUNX1 primary ALL samples and the REH cell line using single cell RNA-seq (scRNA-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

15 Samples

Download data: BIGWIG, MTX, TSV

(Submitter supplied) [Gro-seq] Precursor B acute leukemia cells measured using global nuclear run-on sequencing [ChIP-Seq] The genome-wide occupancy of ser2 and ser5 phosphorylated RNA pol2 and H3K4me3 was measured in precursor B acute leukemia cells measured using chip-seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

21 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) We analyzed 52 Diagnostic samples from childhood Acute lymphoblastic leukemia samples

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

52 Samples

Download data: CSV

(Submitter supplied) There is increasing evidence that microRNA and transcription factors interact in an instructive fashion in normal and malignant hematopoiesis. We explored the impact of TEL-AML1 (ETV6-RUNX1), the most common fusion protein in childhood leukemia, on miRNA expression and the leukemic phenotype. Using RNA interference, miRNA expression arrays, and quantitative PCR, we identified miRNA-494 and miRNA-320a to be upregulated upon TEL-AML1 silencing independently of TEL expression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10861

2 Samples

Download data: TXT

(Submitter supplied) A heterogeneous genetic subtype of B-cell precursor acute lymphoblastic leukemia is driven by constitutive kinase-activation, including patients with JAK2 fusions. In our study, we model the impact of a novel JAK2 fusion protein on hematopoietic development in human induced pluripotent stem cells (hiPSCs). We insert the RUNX1-JAK2 fusion into one endogenous RUNX1 allele through employing in trans paired nicking genome editing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TXT

(Submitter supplied) This file contains the gene expression data for 654 pediatric acute lymphoblastic leukemia samples

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

654 Samples

Download data: CEL

(Submitter supplied) The t(12;21) translocation is the most common genetic rearrangement in childhood acute lymphoblastic leukemia (ALL) and gives rise to the TEL-AML1 fusion gene, which functions as a transcription factor. TEL-AML1 expression in EML1 cells results in an impairment of differentiation along the B-lymphoid lineage.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5661

Platform:

GPL11533

12 Samples

Download data: CEL

Analysis of TEL-AML1 oncogene-expressing hematopoietic stem/progenitor cell line EML1 treated with interleukin 7 (IL7) and FLT3 ligand (FLT3L) for up to 7 days. IL7 and FLT3L treatment induces B-cell differentiation. Results provide insight into the role of TEL-AML1 in early B-cell differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation, 2 protocol, 3 time sets

Platform:

GPL11533

Series:

GSE64919

12 Samples

Download data: CEL

(Submitter supplied) Background: The most common rearrangement in childhood precursor B-cell acute lymphoblastic leukemia (pre-B ALL) is the t(12;21)(p13;q22) translocation resulting in the ETV6-AML1 fusion gene. A frequent concomitant event is the loss of the residual ETV6 allele suggesting a critical role for the ETV6 transcriptional repressor in the etiology of pre-B ALL. However, the precise mechanism through which loss of functional ETV6 contributes to disease pathogenesis is still unclear Results: To investigate the impact of ETV6 loss on the transcriptional network and identify new transcriptional targets of ETV6, we used whole transcriptome analysis of both pre-B leukemic cell lines and pre-B ALL patients combined with chromatin immunoprecipitation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL16558

25 Samples

Download data: TXT

(Submitter supplied) B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic origin of the disease remains unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. We assessed the DNA methylation status of 402,842 CpG-sites across the genome (Illumina 450k array) in tumor and remission samples of 46 pre-B ALL patients, thus generating the most comprehensive single CpG-site resolution pre-B ALL methylomes so far. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

92 Samples

Download data: TXT

(Submitter supplied) Acute lymphoblastic pediatric leukemia specimens without known genetic hallmarks are examined for hidden genomic aberrancies and related gene expression profiles Integration of genomic variation and gene expression profiling identifies hidden genetic lesions and novel pathways involved in BP-ALL pathogenesis Keywords: expression data

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL570 GPL2004 GPL2005

160 Samples

Download data: CEL, CHP, PDF

(Submitter supplied) Gene expression profiling of normal hematopoietic cell subpopulations RNA extracted from flow sorted normal hematopietic cells were hybridized onto Affymetrix U133 Plus 2.0 arrays.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

16 Samples

Download data: CEL

(Submitter supplied) Germline mutations in ETV6 are associated with a syndrome of thrombocytopenia and leukemia predisposition, and ETV6 is among the most commonly mutated genes in leukemias, especially childhood B cell acute lymphoblastic leukemia. However, the mechanisms underlying disease due to ETV6 dysfunction are poorly understood. In order to address these gaps in knowledge, using CRISPR/Cas9, we developed a mouse model of the most common recurrent, disease-causing germline mutation in ETV6, which recapitulates aspects of human disease. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

21 Samples

Download data: TXT

(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; Third-party reanalysis

Platforms:

GPL18573 GPL24676 GPL16791

97 Samples

Download data: BW, SF

(Submitter supplied) Distal enhancers play critical roles in sustaining oncogenic gene expression programs. We obtained ATAC-Seq data and ChIP-Seq data using antibodies against the H3K27ac histone mark, transcription factors ERG and ETV6, and input chromatin from B-ALL cell lines and comparator B-cell cancer cell lines, including B-ALL with biallelic ETV6 inactivation, ETV6-RUNX1, and intact ETV6. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1+ and ETV6-null B-ALL. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL18573 GPL16791 GPL24676

56 Samples

Download data: BW, TXT