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| 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.
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| 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.
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| |
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| Contributor(s) |
Ghazavi F, Van Loocke W, Van Vlierberghe P, De Moerloose B, Lammens T, Benoit Y, Speleman F |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Farzaneh Ghazavi |
| E-mail(s) |
farzaneh.ghazavi@ugent.be
|
| Organization name |
Gent university hospital
|
| Department |
Center of medical genetics
|
| Street address |
De Pintelaan 185
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (27)
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| This SubSeries is part of SuperSeries: |
| GSE79873 |
Unique long non-coding RNA expression signature in ETV6/RUNX1-driven B-cell precursor acute lymphoblastic leukemia |
|
| Relations |
| BioProject |
PRJNA317295 |
| SRA |
SRP072825 |
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