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Series GSE79872 Query DataSets for GSE79872
Status Public on Sep 26, 2016
Title RNA-sequencing of B-ALL cell lines, REH treated with LNA GapmeRs against four lncRNAs
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their expression and role in pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1 positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. An ETV6/RUNX1 expression signature was established, consisting of 596 lncRNAs (434 up and 162 down) using expression analysis of a series of primary patient samples. Subsequently, RNA sequencing from BCP-ALL cell lines and shRNA-mediated silencing of ETV6/RUNX1, illustrated that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 are bona fide ETV6/RUNX1 targets and could serve as novel biomarkers of this prevalent subtype of human leukemia.
Overall design REH cell lines were treated with LNA GapmeRs. Cells were collected 72h after treatment. This was performed for 3 replicates. RNA-sequencing was performed on these samples.
Contributor(s) Ghazavi F, Van Loocke W, Van Vlierberghe P, De Moerloose B, Lammens T, Benoit Y, Speleman F
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Submission date Apr 04, 2016
Last update date May 15, 2019
Contact name Farzaneh Ghazavi
Organization name Gent university hospital
Department Center of medical genetics
Street address De Pintelaan 185
City Ghent
ZIP/Postal code 9000
Country Belgium
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (27)
GSM2107716 No LNA-rep1
GSM2107717 NTC-rep1
GSM2107718 lnc-TIMM21-LNA1-rep1
This SubSeries is part of SuperSeries:
GSE79873 Unique long non-coding RNA expression signature in ETV6/RUNX1-driven B-cell precursor acute lymphoblastic leukemia
BioProject PRJNA317295
SRA SRP072825

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Supplementary file Size Download File type/resource
GSE79872_RAW.tar 8.6 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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