GEO DataSets

Analysis of tumor cells from pediatric patients with early T-cell precursor acute lymphoblastic leukemia (ETP ALL). The ETP ALL subtype has a poor prognosis when treated with standard chemotherapy. Results provide insight into the molecular mechanisms underlying ETP ALL.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 disease state sets

Platform:

GPL13158

Series:

GSE28703

52 Samples

Download data: CEL

(Submitter supplied) Acute lymphoblastic leukaemia with early T-cell precursor immunophenotype (ETP ALL) is a highly aggressive subtype of ALL of unknown aetiology. To gain insights into the genetic basis of this disease, we performed whole genome sequencing of tumour and normal DNA of 12 children with ETP ALL. Analysis of structural and sequence variants in this discovery cohort, and mutation recurrence screening in a panel of 51 ETP and 43 non ETP ALL samples identified a high frequency of activating mutations in genes regulating cytokine receptor and Ras signalling, including IL7R, NRAS, KRAS, FLT3, BRAF, JAK1 and JAK3 in ETP ALL. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

575 Samples

Download data: CEL

(Submitter supplied) Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole genome sequencing of tumour and normal DNA from 12 children with ETP ALL and assessed the frequency of somatic alterations in 52 ETP and 42 non-ETP T-ALL samples by sequencing and DNA copy number analysis. ETP ALL was characterised by a high frequency of activating mutations in genes regulating cytokine receptor and Ras signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF); alterations disrupting haemopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1, EP300); and inactivating mutations in histone modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4299

Platform:

GPL13158

52 Samples

Download data: CEL

(Submitter supplied) The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure. Based on the hypothesis that microarrays might identify patients who fail therapy, we used the Affymetrix U133 Plus 2.0 chip and prediction analysis of microarrays (PAM) to profile 50 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Study 9404. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL96

92 Samples

Download data: CEL

(Submitter supplied) The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure. Based on the hypothesis that microarrays might identify patients who fail therapy, we used the Affymetrix U133 Plus 2.0 chip and prediction analysis of microarrays (PAM) to profile 50 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Study 9404. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

50 Samples

Download data: CEL

(Submitter supplied) The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure. Based on the hypothesis that microarrays might identify patients who fail therapy, we used the Affymetrix U133 Plus 2.0 chip and prediction analysis of microarrays (PAM) to profile 50 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Study 9404. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

42 Samples

Download data: CEL

(Submitter supplied) To investigate the role of BCL11B in the initial stages of human thymopoiesis, we performed loss of function (knockdown) studies in an in vitro human thymopoiesis model (cord blood CD34+ cells co-cultured on OP9DLL1 stromal cell line). Gene expression profiling by RNA-Seq demonstrated that BCL11B knockdown resulted in downregulation of T-lineage genes and upregulation of stem cell, myeloid and NK genes, indicating BCL11B is required for the establishment of a T-lineage commitment transcriptional program.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 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

Platform:

GPL18573

26 Samples

Download data: TXT

(Submitter supplied) To define binding targets during thymopoiesis on a genome wide scale, we performed ChIP-Seq for BCL11B on two cell types isolated from the human thymus: the CD34+ progenitors and the more differentiated CD34- cells

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) To investigate the effects of BCL11B on T-cell differentiation, we performed gain of function studies in cells with a T-lineage differentiation arrest, namely T-ALL cells. Gene expression profiling by RNA-Seq demonstrated that BCL11B overexpression induced transcriptional changes consistent with T-cell differentiation as early as 72 hours after transduction, indicating a rapid regulatory effect of BCL11B on the T-lineage transcriptional program and supporting an important role for BCL11B in human T-cell differentiation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 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

Platform:

GPL13112

8 Samples

Download data: BW, TXT

(Submitter supplied) Purpose: To characterize transcriptional changes associated with homozygous inactivation the Polycomb Repressive Complex 2 (PRC2) lysine methyltransferase Ezh2 in a mouse model of earlt T-cell precursor ALL (ETP-ALL) Methods: We sequenced mRNA from NRASQ61K transformed murine LSK-cells co-transduced with a self-inactivating Cre-vector. Cells were sorted for Cre-expression (lox-stop-loxRosa26-YFP) or expression of an inert control vector (GFP) and differentiated on OP9DL1 stroma with and without a functional Ezh2 gene. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Purpose: To characterize changes in genome-wide H3K27me3 associated with homozygous inactivation the Polycomb Repressive Complex 2 (PRC2) lysine methyltransferase Ezh2 in a mouse model of earlt T-cell precursor ALL (ETP-ALL) Methods: We performed Chip-seq for the H3K27me3 Chromatin mark on Ezh2ff and Ezh2ko cells NRASQ61K leukemias. Results: Inactivation of Ezh2 in this model leads to accelerated leukemia development. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BW, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Genome variation profiling by SNP array; SNP genotyping by SNP array

4 related Platforms

42 Samples

Download data: CEL, CYCHP, TXT

(Submitter supplied) This study identified a cytogenetic-molecular entity, we named BCL11B-R, that showed a typical constellation of genomic features, namely BCL11B activation via chromosome translocations at 14q32, a distinct transcriptome profile, and FLT3 mutations.

Organism:

Homo sapiens

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL15520

15 Samples

Download data

(Submitter supplied) This study identified a cytogenetic-molecular entity, we named BCL11B-R, that showed a typical constellation of genomic features, namely BCL11B activation via chromosome translocations at 14q32, a distinct transcriptome profile, and FLT3 mutations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) This study identified a cytogenetic-molecular entity, we named BCL11B-R, that showed a typical constellation of genomic features, namely BCL11B activation via chromosome translocations at 14q32, a distinct transcriptome profile, and FLT3 mutations.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16131 GPL11157

15 Samples

Download data: CEL, CYCHP

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Genome variation profiling by genome tiling array; Methylation profiling by array; Other

5 related Platforms

171 Samples

Download data: HIC, IDAT, NARROWPEAK, RDS, TXT

(Submitter supplied) CCCTC-binding factor (CTCF) regulates the 3D chromatin architecture by facilitating chromosomal loops. In addition to insulation of euchromatin from heterochromatin, CTCF is an important transcription factor and regulator of antigen receptor and T cell receptor recombination events. CTCF inactivating events have been found in human cancer, resulting in deregulation of global gene expression by altered methylated genomic states. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

8 Samples

Download data: HIC

(Submitter supplied) CCCTC-binding factor (CTCF) regulates the 3D chromatin architecture by facilitating chromosomal loops. In addition to insulation of euchromatin from heterochromatin, CTCF is an important transcription factor and regulator of antigen receptor and T cell receptor recombination events. CTCF inactivating events have been found in human cancer, resulting in deregulation of global gene expression by altered methylated genomic states. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

36 Samples

Download data: RDS