Study

Linking the epigenetic landscape in chronic lymphocytic leukemia to deregulated chromatin networks

Study ID Alternative Stable ID Type
EGAS00001002518 Other

Study Description

Aberrant chromatin features and epigenetic signaling emerge as an important part of the tumor disease state in chronic lymphocytic leukemia (CLL). However, an integrative analysis of the malignant chromatin landscape is currently missing. Here, we mapped DNA-methylation, nucleosome position, 7 histone modifications, ATAC-seq and the transcriptome in primary CD19+ sorted B-cells from the peripheral blood of CLL patients in comparison to non-malignant lymphocytes of healthy donor reference samples. On the > 50 kb scale we identified global differences with respect to DNA methylation, nucleosome positioning and histone modifications in CLL. Furthermore, a chromatin state annotation was developed to identify deregulated chromatin features of promoters and enhancers in CLL. By integrating these findings with an ATAC-seq based transcription factor binding analysis we identified a set of promoters and enhancers specific to CLL that were enriched in certain transcription factors binding motifs and genes of the BCR signaling pathway. Thus, our study provides an in-depth map of the CLL ... (Show More)

Study Datasets 7 datasets.

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Dataset ID Description Technology Samples
EGAD00001003421
Sequence data of 28 Samples (19 chronic lymphocytic leukemia, 9 control) Including RNA-Seq and ChIP-Seq of following histone modifications: H3, H3K4me1, H3K4me3, H3K9ac, H3K9me3, H3K27ac, H3K27me3, H3K36me3 Project see: http://www.cancerepisys.org/
28
EGAD00001005965
Single-cell ATAC-seq data for 5 CLL samples (2 controls, 3 tumor) of the CancerEpiSys-PRECiSe project.
Illumina HiSeq 2000 5
EGAD00001005966
Tagged-WGBS for 3 Naive B Cell samples of the CancerEpiSys-PRECiSe project.
Illumina HiSeq 2000 3
EGAD00001005967
ATAC-seq data for 26 CLL samples (7 controls, 19 tumor) of the CancerEpiSys-PRECiSe project.
Illumina HiSeq 2000,Illumina HiSeq 4000 26
EGAD00001005968
long RNA data for 27 CLL samples (8 controls, 19 tumor) of the CancerEpiSys-PRECiSe project.
Illumina HiSeq 2000 27
EGAD00001005969
ChIPseq data for 31 CLL samples (12 controls, 19 tumor) of the CancerEpiSys-PRECiSe project; containing histone H3, histone modifications and transcription factor binding sites (CTCF, EBF1).
Illumina HiSeq 2000,NextSeq 550 31
EGAD00001005970
WGBS data for 75 paired fastq, spread over 31 samples (4 healthy T-cell, 7 healthy B-cell, 20 B-cell CLL tumors) of the CancerEpiSys-PRECiSe project.
Illumina HiSeq 2000 31

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