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Series GSE110634 Query DataSets for GSE110634
Status Public on Sep 11, 2018
Title Total RNA-seq in ALL-SIL upon JQ1 inhibition
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of blood cancer resulting from malignant transformation of T-cell precursors. Several oncogenes, including the ‘T-cell leukemia homeobox 1’ TLX1 (HOX11) transcription factor, have been identified as early driver events that cooperate with other genetic aberrations in leukemic transformation of progenitor T-cells. The TLX1 controlled transcriptome in T-ALL has been investigated extensively in the past in terms of protein-coding genes, but remains unexplored thus far at the level of long non-coding RNAs (lncRNAs), the latter renown as well-established versatile and key players implicated in various cancer hallmarks. In this study, we present the first extensive analysis of the TLX1 regulated transcriptome focusing on lncRNA expression patterns. We present an integrative analysis of polyA and total RNA sequencing of ALL-SIL lymphoblasts with perturbed TLX1 expression and a primary T-ALL patient cohort (including 5 TLX1+ and 12 TLX3+ cases). We expanded our initially presented dataset of TLX1 and H3K27ac ChIP data in ALL-SIL cells (Durinck et al., Leukemia, 2015) with H3K4me1, H3K4me3, and ATAC-seq data to accurately define (super-) enhancer marked lncRNAs and assigned potential functional annotations to candidate TLX1-controlled lncRNAs through an in silico guilt-by-association approach. Our study paves the way for further functional analysis of selected lncRNAs as potential novel therapeutic targets for a precision medicine approach in the context of T-ALL.
 
Overall design Total RNA-seq data was generated for the T-ALL cell line ALL-SIL upon JQ1 inhibition
 
Contributor(s) Verboom K, Van Loocke W, Volders P, Decaesteker B, Soulier J, Van Vlierberghe P, Vandesompele J, Speleman F, Durinck K
Citation(s) 29954933
Submission date Feb 14, 2018
Last update date Mar 26, 2019
Contact name Karen Verboom
E-mail(s) karen.verboom@ugent.be
Organization name Ghent University
Department Pediatrics and Genetics
Lab Center for Medical Genetics Ghent
Street address De Pintelaan 185
City Ghent
ZIP/Postal code 9000
Country Belgium
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM3004605 JQ1_rep1
GSM3004606 JQ1_rep2
GSM3004607 JQ1_rep3
This SubSeries is part of SuperSeries:
GSE110637 T-ALL
Relations
BioProject PRJNA434173
SRA SRP132969

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
GSE110634_RAW.tar 2.1 Mb (http)(custom) TAR (of TAB)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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