GEO DataSets

(Submitter supplied) Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL6604

186 Samples

Download data: PAIR

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL6604

380 Samples

Download data: PAIR

(Submitter supplied) Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL6604

194 Samples

Download data: PAIR

(Submitter supplied) Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

154 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6102 GPL6801 GPL8490

69 Samples

Download data: CEL, CHP

(Submitter supplied) Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

19 Samples

Download data: CEL, CHP

(Submitter supplied) Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

25 Samples

Download data: TXT

(Submitter supplied) Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

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) The aggressive MLL-rearranged leukemias are well-known for their unique gene-expression profiles. The goal of this study was to characterize the MLL-specific DNA methylation profiles in infant acute lymphoblastic leukemia (ALL). Genome-wide DNA methylation profiling was performed on primary infant ALL samples. The majority of infant ALL samples demonstrated severe DNA hypermethylation compared with normal pediatric bone marrows, which implies that targeting of DNA methylation may be an interesting option for future therapeutic strategies in MLL-rearranged infant ALL. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL4126

60 Samples

Download data: TXT

(Submitter supplied) PAPER 1:"Identification of novel subgroups of high-risk pediatric precursor B acute lymphoblastic leukemia (B-ALL) by unsupervised microarray analysis: clinical correlates and therapeutic implications. A Children's Oncology Group (COG) study." ABSTRACT We examined gene expression profiles of pre-treatment specimens from 207 patients from the COG P9906 study to identify signatures of children with high risk B-precursor acute lymphoblastic leukemia (ALL) and to determine whether the resulting clusters are associated with either specific clinical features or treatment response characteristics. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

207 Samples

Download data: CEL, CHP, MSK

(Submitter supplied) Acute lymphoblastic leukemia (ALL) is the most common cancer in children. We applied WGBS and the informME analysis pipeline to investigate the role of DNA methylation stochasticity in pre-B cell ALL.

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

53 Samples

Download data: BW, XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL6604 GPL11219

24 Samples

Download data: PAIR

(Submitter supplied) DNA methylation analysis on purified human long-term and short-term hematopoietic stem cells (LT-HSC, ST-HSC), common myeloid and megakaryocyte-erythrocyte progenitor cells (CMP, MEP) using HELP arrays. FACS-purified hematopoietic stem and progenitor cell (HSPC) subsets were analyzed for changes in DNA methylation using NimbleGen HELP microarrays.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL6604

12 Samples

Download data: PAIR

(Submitter supplied) RNA expression analysis on purified human long-term and short-term hematopoietic stem cells (LT-HSC, ST-HSC), common myeloid and megakaryocyte-erythrocyte progenitor cells (CMP, MEP) using microarrays. FACS-purified hematopoietic stem and progenitor cell (HSPC) subsets were analyzed for changes in RNA expression using NimbleGen gene expression microarrays.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11219

12 Samples

Download data: PAIR

(Submitter supplied) We have used a human gene promoter tiling microarray platform to analyze a cell line model of lymph node metastasis comprised of a poorly metastatic MDA-MB-468GFP human breast adenocarcinoma cell line and its highly metastatic variant (468LN). Gene networks and pathways associated with metastasis were identified and target genes associated with epithelial-mesenchymal transition (EMT) was validated with respect to DNA methylation effects on gene expression. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL5082

6 Samples

Download data: CEL, TXT

(Submitter supplied) We developed and validated a diagnostic miniarray to recognize different subtypes of ALL. We analyzed blindly the gene expression profiling of 17 patients: 10 ALL-B, 5 ALL-T and 2 MLL/AF4. This miniarray was able to assign all samples to the correct class. We compared the transcription profiles of the leukemic samples by miniarray competitive hybridisation against an arbitrary total RNA reference prepared from normal human bone marrow. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2016

17 Samples

Download data

(Submitter supplied) We have examined gene expression profiling of 18 children with acute lymphoblastic leukemia (ALL). In particular, the ALL patients are subdivided in three different subtypes by morphological, immunophenotypic and cytogenetical parameters: 10 ALL-B, 5 ALL-T and 3 ALL-B with the specific chromosomal aberration MLL/AF4. We compared the transcription profiles of the leukemic samples by microarray competitive hybridization against an arbitrary total RNA reference prepared from normal human bone marrow. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1235

Platform:

GPL2011

36 Samples

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(Submitter supplied) Miniarray is a diagnostic platform to recognize different subtypes of ALL. It was constructed arraying on glass slides PCR-amplified cDNAs of 30 genes best discriminating ALL-B and ALL-T patients, 10 tags that are differentially expressed in all leukemia samples and 9 housekeeping genes used as hybridization controls. PCR products are printed in quadruplicate in each miniarray and each slide contains four miniarrays. more...

Organism:

Homo sapiens

1 Series

17 Samples

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