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Series GSE87283 Query DataSets for GSE87283
Status Public on Jun 26, 2017
Title RUNX1-ETO and RUNX1-EVI-1 differentially program the chromatin landscape in t(3;21) and t(8;21) AML but share global C/EBP-alpha dysfunction (ChIP-Seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary RUNX1 is a frequent target of translocations in acute myeloid leukemia whereby its DNA binding domain fuses to different epigenetic regulators. To assess how different RUNX1 fusion proteins interact with the epigenome we compared the global binding patterns and the chromatin landscape of t(8;21) and t(3;21) AML which express RUNX1-ETO and RUNX1-EVI-1, respectively. We found that differential prognosis for these types of AML is reflected in fundamental differences in gene expression, chromatin landscape, binding patterns of the fusion proteins and other transcription factors as identified by genome-wide digital footprinting in patients. As previously shown for RUNX1-ETO, knockdown of RUNX1-EVI-1 expression initiates differentiation of t(3;21) cells which is associated with up-regulation of genes vital for myeloid differentiation, including C/EBPα. Furthermore, by expressing either dominant-negative C/EBP or an inducible C/EBPα construct in t(3;21) cells we show that C/EBPα is necessary and sufficient for the differentiation response of these cells to RUNX1-EVI-1 knockdown.
 
Overall design ChIP-seq expreiments have been used to study the chromatin landscape of t(8;21) and t(3;21) AML
 
Contributor(s) Loke JC, Assi SA, Imperato MR, Ptasinska A, Cauchy P, Raghavan M, Delwel HR, Cockerill PN, Heidenreich O, Bonifer C
Citation(s) 28538183
Submission date Sep 22, 2016
Last update date May 15, 2019
Contact name Salam Adli Assi
E-mail(s) s.a.assi@bham.ac.uk
Organization name University of Birmingham
Department Institute for Cancer and Genomic Sciences
Street address IBR
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (10)
GSM2326835 Anti-EVI1_sKH1_ChIPseq
GSM2326836 Anti-RUNX1_sKH1_ChIPseq
GSM2326837 sKH1_Anti-EVI1_SIMM_D10_ChIPseq
This SubSeries is part of SuperSeries:
GSE87286 RUNX1-ETO and RUNX1-EVI-1 differentially program the chromatin landscape in t(3;21) and t(8;21) AML but share global C/EBP-alpha dysfunction
Relations
BioProject PRJNA343970
SRA SRP090330

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
GSE87283_RAW.tar 1.8 Gb (http)(custom) TAR (of BW, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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