GEO DataSets

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL21290

138 Samples

Download data: BIGWIG, CSV, NARROWPEAK

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

188 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: MTX, TSV

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

176 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral-blood B cells from patients with chronic lymphocytic leukaemia (CLL) and healthy individuals at single base pair resolution. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

26 Samples

Download data: BED, BW

(Submitter supplied) In chronic lymphocytic leukemia (CLL) a diverse set of genetic mutations is embedded in a deregulated epigenetic landscape that drives cancerogenesis. To elucidate the role of aberrant chromatin features, we mapped DNA methylation, 7 histone modifications, nucleosome positions, chromatin accessibility, binding of EBF1 and CTCF as well as the transcriptome of B cells from CLL patients and healthy donors. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL11154

519 Samples

Download data: BIGBED, BW

(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:

GPL16699 GPL10878

40 Samples

Download data: TXT

(Submitter supplied) In the present study, the methylation profiling (MeDIP) was carried out in 14 treatment-naive, early stage (Rai stage 0-2) CLL patients and pooled 19+ normal controls. To find an association of methylation with IGHV mutation status, CLL patients were further segregated into IGHV unmutated (n=9) and IGHV mutated (n=5) subgroups. The methylation signature obtained for CLL versus nornal controls and; unmutated versus mutated CLL was integrated with gene expression profile of these patients and the results were correlated with clinical outcome.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL10878

17 Samples

Download data: TXT

(Submitter supplied) In the present study, the gene expression profiling was carried out in 21 early stage CLL patients. A gene expression signature was generated for CLL patients as compared to normal controls; CLL patients were further seggregated into IGHV unmutated (n=10) and IGHV mutated (n=11) subgroups. The expression pattern was confirmed using real time quantitative PCR and the results were correlated with clinical outcome.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16699

23 Samples

Download data: TXT

(Submitter supplied) We propose a computational method for single cell comparative regulatory analysis based on single cell gene expression (scRNA-seq) and single cell chromatin accessibility data (scATAC-seq) from two different conditions. Our software sc-compReg provides joint clustering and embedding of the cells from both scRNA-seq and scATAC-seq, and construction of differential regulatory networks across two conditions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

4 Samples

Download data: BED, MTX, TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL8227 GPL6244

310 Samples

Download data: CEL, TXT

(Submitter supplied) Prospective series of 136 clinical monoclonal B lymphocytosis (cMBL) and 216 chronic lymphocytic leukemia (CLL) Rai 0 patients, were investigated in this study. While the distribution of CD38 and ZAP-70 positivity was similar, IGHV-mutated cases were more frequent among cMBL (P = 0.005). A Cox multivariate analysis on the whole patient cohort showed that cMBL condition was predictive of longer PFS, while CD38 expression and IGHV-unmutated status and CD38 expression correlated significantly with a shorter PFS in cMBL and Rai0-CLL, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

160 Samples

Download data: CEL

(Submitter supplied) Prospective series of 136 clinical monoclonal B lymphocytosis (cMBL) and 216 chronic lymphocytic leukemia (CLL) Rai 0 patients, were investigated in this study. While the distribution of CD38 and ZAP-70 positivity was similar, IGHV-mutated cases were more frequent among cMBL (P = 0.005). A Cox multivariate analysis on the whole patient cohort showed that cMBL condition was predictive of longer PFS, while CD38 expression and IGHV-unmutated status and CD38 expression correlated significantly with a shorter PFS in cMBL and Rai0-CLL, respectively. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8227

150 Samples

Download data: TXT

(Submitter supplied) Glucocorticoids are part of the therapeutic armamentarium of chronic lymphocytic leukemia where it has been suggested that cells with unmutated IGHV genes exhibit higher sensitivity. The mechanisms by which glucorticoids are active in CLL are not well elucidated. We used microarrays to detail the global programme of gene expression underlying dexamethasone differential activity according to the prognostic subgroups mutated IGHV genes / low ZAP-70 expression and unmutated IGHV genes / high ZAP-70 expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

24 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL20795 GPL24676

32 Samples

Download data: BIGWIG

(Submitter supplied) Nasopharyngeal carcinoma (NPC) is enedemic in Southeast Asia but is uncommon worldwide. In Hong Kong, approximately 95% of NPC cases are associated with Esptein-Barr Virus (EBV). EBV has been shown to induce changes in the epigenetics of EBV-malignancies. Epigenetics in NPC may thus play an important role in NPC pathogensis. We performed whole-genome bisulfite sequencing (WGBS) to profile the methylation changes in NPC and investigate the role of abberant methylation pattern in NPC.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

20 Samples

Download data: BIGWIG

(Submitter supplied) Nasopharyngeal carcinoma (NPC) is enedemic in Southeast Asia but is uncommon worldwide. In Hong Kong, approximately 95% of NPC cases are associated with Esptein-Barr Virus (EBV). EBV has been shown to induce changes in the epigenetics of EBV-malignancies. Epigenetics in NPC may thus play an important role in NPC pathogensis. We performed targeted bisulfite sequencing to accurately profile the methylation changes in NPC and investigate the role of abberant methylation pattern in NPC.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: BIGWIG

(Submitter supplied) Purpose: Multiple myeloma is a malignancy of plasma cells. Extensive genetic and transcriptional characterization of myeloma has identified subtypes with prognostic and therapeutic implications. In contrast, relatively little is known about the myeloma epigenome. Experimental Design: CD138+CD38+ myeloma cells were isolated from fresh bone marrow aspirate or the same aspirate after freezing for one to six months. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

33 Samples

Download data: CSV

(Submitter supplied) Cancer evolution is fueled by genetic and epigenetic diversity, and intra-tumoral heterogeneity in DNA methylation has been shown to co-operate with genetic heterogeneity to empower evolutionary capacity of cancers such as chronic lymphocytic leukemia. Here, we show that epigenetic diversification leads to decreased coordination across layers of epigenetic information, likely reflecting an admixture of cells with diverging epigenetic identities. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

90 Samples

Download data: BW, TXT

(Submitter supplied) Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer. In addition to genetic mutations, chronic lymphocytic leukemia (CLL) undergoes diversification through stochastic DNA methylation changes – epimutations. To measure the epimutation rate at single-cell resolution, we applied multiplexed reduced representation bisulfite sequencing (MscRRBS) to healthy donors B cells and CLL patient samples. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

843 Samples

Download data: CSV, TXT, XLSX