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Series GSE113336 Query DataSets for GSE113336
Status Public on May 22, 2019
Title Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary 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. A globally increased histone deacetylase activity was detected and half of the genome comprised transcriptionally downregulated partially DNA methylated domains demarcated by CTCF. CLL samples displayed a H3K4me3 redistribution and nucleosome gain at promoters as well as changes of enhancer activity and enhancer linkage to target genes. A DNA binding motif analysis identified transcription factors that gained or lost binding in CLL at sites with aberrant chromatin features. These findings were integrated into a gene regulatory enhancer containing network enriched for B cell receptor signaling pathway components. Our study predicts novel molecular links to targets of CLL therapies and provides a valuable resource for further studies on the epigenetic contribution to the disease.

Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D & Rippe K (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks. Mol Syst Biol 15, e8339. doi: 10.15252/msb.20188339
 
Overall design We analyzed a carefully selected cohort of clinically and genetically fully characterized primary leukemia cells in bulk samples and at the single cell level for genome-wide DNA-methylation, nucleosome position, DNA-accessibility by ATAC-seq, the 7 most relevant histone modifications plus CTCF and EBF1 by ChIPseq as well as the transcriptome. Raw sequencing data for all the samples are available at the European Genome-phenome Archive (http://www.ebi.ac.uk/ega/), under the accession number EGAS00001002518.
Web link http://www.cancerepisys.org/
 
Contributor(s) Mallm J, Iskar M, Ishaque N, Klett L, Kugler SJ, Muino JM, Teif V, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K
Citation(s) 31118277
Submission date Apr 18, 2018
Last update date Jul 11, 2019
Contact name Karsten Rippe
Phone +49-6221-54-51376
Organization name DKFZ
Department Division of Chromatin Networks
Street address Im Neuenheimer Feld 267-BQ24
City Heidelberg
State/province Germany
ZIP/Postal code 69120
Country Germany
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (519)
GSM3103405 CES_CX_TechRep1_ATACseq Sample 1
GSM3103406 CES_CX_TechRep2_ATACseq Sample 2
GSM3103407 CES_FG_TechRep1_ATACseq Sample 3
Relations
BioProject PRJNA450852

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE113336_CES_BK_chromHMM.bigbed 5.5 Mb (ftp)(http) BIGBED
GSE113336_CES_CX_chromHMM.bigbed 4.9 Mb (ftp)(http) BIGBED
GSE113336_CES_DT_chromHMM.bigbed 4.9 Mb (ftp)(http) BIGBED
GSE113336_CES_EM_chromHMM.bigbed 5.2 Mb (ftp)(http) BIGBED
GSE113336_CES_FG_chromHMM.bigbed 4.3 Mb (ftp)(http) BIGBED
GSE113336_CES_GN_chromHMM.bigbed 4.5 Mb (ftp)(http) BIGBED
GSE113336_CES_HA_24h_N_chromHMM.bigbed 7.0 Mb (ftp)(http) BIGBED
GSE113336_CES_HA_24h_P_chromHMM.bigbed 4.0 Mb (ftp)(http) BIGBED
GSE113336_CES_HA_2h_N_chromHMM.bigbed 13.2 Mb (ftp)(http) BIGBED
GSE113336_CES_HA_2h_P_chromHMM.bigbed 11.3 Mb (ftp)(http) BIGBED
GSE113336_CES_HA_chromHMM.bigbed 6.1 Mb (ftp)(http) BIGBED
GSE113336_CES_IO_chromHMM.bigbed 5.0 Mb (ftp)(http) BIGBED
GSE113336_CES_JK_24h_N_chromHMM.bigbed 11.6 Mb (ftp)(http) BIGBED
GSE113336_CES_JK_24h_P_chromHMM.bigbed 6.3 Mb (ftp)(http) BIGBED
GSE113336_CES_JK_2h_N_chromHMM.bigbed 8.5 Mb (ftp)(http) BIGBED
GSE113336_CES_JK_2h_P_chromHMM.bigbed 7.4 Mb (ftp)(http) BIGBED
GSE113336_CES_JK_chromHMM.bigbed 8.2 Mb (ftp)(http) BIGBED
GSE113336_CES_KL_chromHMM.bigbed 5.3 Mb (ftp)(http) BIGBED
GSE113336_CES_LM_24h_N_chromHMM.bigbed 5.2 Mb (ftp)(http) BIGBED
GSE113336_CES_LM_24h_P_chromHMM.bigbed 5.3 Mb (ftp)(http) BIGBED
GSE113336_CES_LM_2h_N_chromHMM.bigbed 8.6 Mb (ftp)(http) BIGBED
GSE113336_CES_LM_2h_P_chromHMM.bigbed 6.9 Mb (ftp)(http) BIGBED
GSE113336_CES_LM_chromHMM.bigbed 5.8 Mb (ftp)(http) BIGBED
GSE113336_CES_MA_chromHMM.bigbed 9.5 Mb (ftp)(http) BIGBED
GSE113336_CES_NQ_chromHMM.bigbed 4.1 Mb (ftp)(http) BIGBED
GSE113336_CES_OZ_chromHMM.bigbed 5.3 Mb (ftp)(http) BIGBED
GSE113336_CES_PP_chromHMM.bigbed 5.1 Mb (ftp)(http) BIGBED
GSE113336_CES_QP_chromHMM.bigbed 4.2 Mb (ftp)(http) BIGBED
GSE113336_CES_QU_chromHMM.bigbed 4.9 Mb (ftp)(http) BIGBED
GSE113336_CES_RC_chromHMM.bigbed 4.6 Mb (ftp)(http) BIGBED
GSE113336_CES_RP_chromHMM.bigbed 4.0 Mb (ftp)(http) BIGBED
GSE113336_CES_TB_chromHMM.bigbed 8.0 Mb (ftp)(http) BIGBED
GSE113336_CES_TH_chromHMM.bigbed 4.8 Mb (ftp)(http) BIGBED
GSE113336_CES_VL_chromHMM.bigbed 5.3 Mb (ftp)(http) BIGBED
GSE113336_CES_WS_chromHMM.bigbed 6.6 Mb (ftp)(http) BIGBED
GSE113336_CES_WW_chromHMM.bigbed 4.8 Mb (ftp)(http) BIGBED
GSE113336_CES_XP_chromHMM.bigbed 5.1 Mb (ftp)(http) BIGBED
GSE113336_CES_YF_chromHMM.bigbed 5.6 Mb (ftp)(http) BIGBED
GSE113336_CES_ZV_chromHMM.bigbed 5.1 Mb (ftp)(http) BIGBED
GSE113336_RAW.tar 357.4 Gb (http)(custom) TAR (of BIGBED, BW)
Raw data not provided for this record
Processed data provided as supplementary file

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