GEO DataSets

(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) 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) Gene expression analyses, were performed on 121 consecutive childhood leukemias (87 B-lineage acute lymphoblastic leukemias (ALLs), 11 T-cell ALLs, and 23 acute myeloid leukemias; AMLs), investigated during an 8-year period at a single center. The supervised learning algorithm k-nearest neighbor (k-NN) was utilized to build gene expression predictors that could classify the ALLs/AMLs according to clinically important subtypes with high accuracy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4861

127 Samples

Download data: TXT

(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) 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) 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) 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) 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

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) Genome binding/occupancy profiling of ETS Variant Transcription Factor 6- Runt Related Transcription Factor 1 fusion protein (ETV6-RUNX1) in REH cells by high throughput sequencing. ETV6-RUNX1 is expressed in pediatric t(12;21) ETV6-RUNX1 B cell precursor acute lymphoblastic leukemia.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18460 GPL16791

2 Samples

Download data: WIG

(Submitter supplied) PAX5 is a tumor suppressor in B-ALL, while the role of PAX5 fusion proteins in B-ALL development is largely unknown. Here we studied the function of PAX5-ETV6 and PAX5- FOXP1 in mice expressing these proteins from the Pax5 locus. Both proteins arrested Blymphopoiesis at the pro-B-to-pre-B cell transition and, contrary to their proposed dominantnegative role, did not interfere with the expression of most Pax5 target genes. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL17021 GPL11002

36 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; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791 GPL15433

38 Samples

Download data: NARROWPEAK

(Submitter supplied) Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. Their pathogenesis is largely unknown, and their treatment is challenging. We have previously discovered the specific association between recurrent t(8;12)(q13;p13) chromosomal translocation, creating ETV6-NCOA2 fusion, with T/Myeloid leukemias. Here we report that the ETV6-NCOA2 initiates T/Myeloid leukemia in preclinical models and examine the expression profile induced by ETV6-NCOA2 in CD34+ cord blood progenitors in-vitro.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

6 Samples

Download data: XLSX

(Submitter supplied) Exparession profiling of lineage negative bone marrow cells from C57B/6 mice expressing either ETV6-NCOA2, KAT6-NCOA2 or empty-vector after five days in in-vitro culture.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: XLSX

(Submitter supplied) Exparession profiling of ETV6-NCOA2 at different stages of disease dEmpty vectorelopment: CD34 cord blood cells transduced with ETV6-NCOA2-GFP or with empty vector-GFP, CD34 cord blood cells transduced with ETV6-NCOA2-NGFR or ETV6-NCOA2-NGFR + NOTCH1-L1601PdP-GFP and transplanted in NSGS mice, and ETV6-NCOA2 patient derived xenografts.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

17 Samples

Download data: XLSX

(Submitter supplied) H3K27Ac ChIP-sequencing of CD34 positive cord blood cells expressing either ETV6-NCOA2 or empty-vector in-vitro and ETV6-NCOA2 patient derived xenograft.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: NARROWPEAK

(Submitter supplied) Early immature T-cell acute lymphoblastic leukemias (T-ALLs) account for about 5-10% of pediatric T-ALLs and are associated with poor prognosis. However, the genetic defects that drive the biology of these tumors remain largely unknown. Analysis of microarray gene expression signatures in adult T-ALL demonstrated a high prevalence of early immature leukemias and revealed a close relationship between these tumors and myeloid leukemias. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

20 Samples

Download data: CEL

(Submitter supplied) Transcriptional effects of ETV6 inactivation in immature T-ALL were investigated by gene expression analysis upon siRNA-mediated knockdown of ETV6 in LOUCY cells, a T-ALL cell line with a transcriptional program highly related to that of immature T-ALLs. Gene Set Enrichment Analysis (GSEA) of the ETV6 knockdown signature showed a significant enrichment in genes characteristically upregulated in ETV6 mutant immature T-ALLs including HOXA13, PRDM16, PTEN and CD33.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

4 Samples

Download data: TXT

(Submitter supplied) Analysis of microarray gene expression signatures in adult T-ALL demonstrated a high prevalence of early immature leukemias and revealed a close relationship between these tumors and myeloid leukemias.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

57 Samples

Download data: TXT