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Series GSE73845 Query DataSets for GSE73845
Status Public on May 12, 2016
Title Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines [HTS]
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Cancer stem cells (CSC) dictate tumor cell heterogeneity in diverse cancer types and arise, in part, from microRNA (miRNA)-dependent alteration of gene expression. The let-7 miRNA family induces differentiation by silencing genes that maintain stemness and is repressed by the RNA-binding proteins LIN28A/B, which preserve stemness in normal embryonic and malignant cells. Here, we observed that LIN28A/B is undetectable in glioma stem cells (GSC) whereas let-7 and, paradoxically, their target genes are highly expressed. Using photoactivatable-ribonucloside-enchanced crosslinking and immunoprecipitation (PAR-CLIP), we show that insulin-like growth factor-2 mRNA-binding protein 2 (IMP2) protects let-7 target genes from silencing and provides a mechanistically distinct alternative to LIN28A/B toward both GSC and neural stem cell specification. Our observations define the RNA-binding repertoire of IMP2 and identify a mechanism by which it supports GSC maintenance.
 
Overall design We characterized RNA binding sites of IMP2 in MGG8 Glioma cancer stem cells and differentiated cells. To profile changes upon IMP2 modulation we performed RNA-Seq in MGG4 and 8 cells in both states upon IMP2 knockdown and overexpression. Furthermore we investigated changes during differentiation from cancer stem cells to adherent cells in 6 and 7 RNA-Seq datasets in MGG4 and 8 cells.
 
Contributor(s) Degrauwe N, Schlumpf TB, Paro R, Stamenkovic I
Citation(s) 27184842
Submission date Oct 08, 2015
Last update date May 15, 2019
Contact name Tommy Beat Schlumpf
Organization name ETH Z├╝rich
Department D-BSSE
Lab Paro
Street address Mattenstrasse 26
City Basel
State/province Basel-Stadt
ZIP/Postal code 4058
Country Switzerland
 
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (25)
GSM1904419 RNA-Seq_MGG4_KD_ctrl [Sample 3]
GSM1904420 RNA-Seq_MGG4_KD [Sample 4]
GSM1904421 RNA-Seq_MGG8_KD_ctrl [Sample 5]
This SubSeries is part of SuperSeries:
GSE73847 Functional characterization of RNA-binding protein IMP2 in primary Glioma cell lines
Relations
BioProject PRJNA298216
SRA SRP064610

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
GSE73845_PARCLIP_IMP2a_r1.bed.gz 1.3 Mb (ftp)(http) BED
GSE73845_PARCLIP_IMP2a_r2.bed.gz 4.6 Mb (ftp)(http) BED
GSE73845_PARCLIP_IMP2s_r1.bed.gz 8.4 Mb (ftp)(http) BED
GSE73845_PARCLIP_IMP2s_r2.bed.gz 6.8 Mb (ftp)(http) BED
GSE73845_RNA_GBM_Diff.txt.gz 1.1 Mb (ftp)(http) TXT
GSE73845_RNA_IMP2a_OE.txt.gz 719.4 Kb (ftp)(http) TXT
GSE73845_RNA_IMP2s_KD.txt.gz 703.0 Kb (ftp)(http) TXT
GSE73845_RNA_brain_IMP2_KO.txt.gz 643.9 Kb (ftp)(http) TXT
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Processed data are available on Series record

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