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Series GSE33912 Query DataSets for GSE33912
Status Public on May 21, 2013
Title Functional Identification of Critical Bmi1 target genes in Neural Progenitor and Malignant Glioma cells
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary In this study, we combined a genome-wide analysis of the Polycomb protein Bmi1 and an in vivo RNAi screening to identify critical targets whose repression in neural progenitor and Malignant Glioma cells enables normal and aberrant self-renewal.
 
Overall design Bmi1 ChIP-sequencing generated in 2 primary adult mouse Neural Progenitor cell lines, 1 mouse astrocytic cell line, 1 mouse Glioma initiating cell line, and 1 mouse Glioma cell line. In human cell lines, Bmi1 ChIP-seq was performed for foetal Neural Progenitor Cells, and 2 Glioblastoma Stem-like cells. ChIP-seq for AP-1 in one Glioblastoma stem-like cell line. ChIP-sequencing were generated using either Illumina GxII or HiSeq. We have further performed RNA-seq of adult Ink4a/Arf -/-;BMI1or GFP dox-inducible shRNA mNPC with a doxycycline inducible shRNA targeting BMI1 or GFP (as control). These cells were either treated with doxyclyine for 48h to ablate BMI1 and GFP expression or further subjected to short-term differentiation using either BMP4 (10ng/ml or 50ng/ml for 3 or 6hrs), or FBS (1 or 10% for 3 or 6hrs). Additional mouse RNA-seq were performed in two biological replica of adult mouse brains (littermate) with either wild-type FVB background or BMI1 -/-. Finally, we performed RNA-seq in human Glioblastoma stem-like cells (most likely belonging to the mesenchymal GBM subtype) treated with BMP7, Arvanil and doxycycline or EtOH treated as ctrl.
 
Contributor(s) Gargiulo G, Cesaroni M, Serresi M, Lancini C, De Vries N, Hulsman D, van Lohuizen M
Citation(s) 23680149
Submission date Nov 23, 2011
Last update date May 15, 2019
Contact name Gaetano Gargiulo
E-mail(s) gaetano.gargiulo@mdc-berlin.de
Organization name Max Delbrüch Center
Department Molecular Oncology
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
 
Platforms (4)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (42)
GSM838662 INK4A/ARF -/- mNPC 1 BMI1
GSM838663 INK4A/ARF -/- mNPC 2 BMI1
GSM838664 INK4A/ARF -/- mGIC BMI1
Relations
SRA SRP009474
BioProject PRJNA148249

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Supplementary file Size Download File type/resource
GSE33912_RAW.tar 54.7 Gb (http)(custom) TAR (of BAM)
GSE33912_fpkm.xlsx.gz 8.0 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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