GEO DataSets

(Submitter supplied) We have found that cyclophilin B (CypB) expression is important for malignant glioblastoma multiforme (GBM) cell proliferation. To identify molecular mechanisms that could explain CypB-dependent survival in human GBM cells, a microarray analysis was performed using RNA prepared from U251MG GBM cells transduced with lentiviral CypB shRNA. These data revealed that about 130 genes were more than 2-fold affected by CypB depletion. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4828

Platform:

GPL10558

6 Samples

Download data: TXT

Analysis of U251 glioblastoma multiforme (GBM) cells depleted for cyclophilin B (CypB), a prolyl isomerase in the endoplasmic reticulum. CypB depletion reduces GBM cell survival. Results provide insight into the role of CypB in the survival of GBM cells.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL10558

Series:

GSE50756

6 Samples

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(Submitter supplied) We performed RNA-seq to determine the impact of FKBP9 depletion on global gene expression profile. The results show knock down of FKBP9 activated ER stress or UPR signaling related genes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21103

42 Samples

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(Submitter supplied) The p53 pathway is a universal tumor suppressor mechanism but the differences of the p53 transcriptional response to oncogenic stress across different tumor types are poorly understood. Using a panel of murine cancer cell lines, we observed that the majority of p53-bound sites were tumor type-specific. Analysis of common p53 targets defined a small but robust core signature and revealed a senescence-specific repression geneset. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

18 Samples

Download data: GTF, TXT

(Submitter supplied) The p53 pathway is a universal tumor suppressor mechanism but the differences of the p53 transcriptional response to oncogenic stress across different tumor types are poorly understood. Using a panel of murine cancer cell lines, we observed that the majority of p53-bound sites were tumor type-specific. Analysis of common p53 targets defined a small but robust core signature and revealed a senescence-specific repression geneset. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

24 Samples

Download data: BED

(Submitter supplied) As a first step towards identifying the target genes of EGFR activity in glioma cells, genome-wide expression analyses were performed using the Affymetrix GeneChip Human Genome U133A array. To accomplish this, mRNA expression levels of these genes were measured in the glioblastoma cell lines, U87 and U178, engineered with EGFR by retrovirus transduction (termed U87-EGFR and U178-EGFR respectively), with or without 20 ng/mL EGF treatment for 3 h.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

8 Samples

Download data: CEL

(Submitter supplied) Microarray was conducted on Illumina Human Ref-6 Version 2 Expression Chip (Illumina, San Diego, CA). Three independent cultures were used for RNA isolation with RNeasy plus mini kit (Qiagen, Valencia, CA). RNA quality was checked by Agilent Bioanalyzer (Agilent, Santa Clara, CA). An Ambion labeling kit was used for labeling cDNA followed by hybridization to Illumina chips. ChIP scan data was extracted by Illumina Beadstudio and subsequently analyzed using Bioconductor lumi package. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

12 Samples

Download data

(Submitter supplied) This study identifies the genes differentially expressed upon MED12 knockdown in A172 glioblastoma cell line. Clariom_S_Human Array was used to assess mRNA expression profile in response to MED12 Knockdown in A172 cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

4 Samples

Download data: CEL

(Submitter supplied) Mutations effects on p53 isoforms’ activities remain largely unknown, although they are mutated in 92% of TP53 mutant cancers. Therefore, exploring the effect of mutations on p53 isoforms activities is a critical, albeit unexplored area in the p53 field. Current glioblastoma treatments, including temozolomide chemotherapy and radiations, induce cellular senescence through a p53-dependent mechanism. Nevertheless, GBMs still have a poor 6.8% five-year survival indicating a need to better understand underlying mechanisms affecting the response to treatments. The progression from low-grade astrocytoma to glioblastoma is accompanied by TP53 mutations. Since Δ133p53α prevents cellular senescence, studying the impact of its mutation in glioblastoma is relevant to determine if it affects the progression and response to treatment of GBM cells. In this aim, we stably overexpressed wild-type (WT) Δ133p53α in WT glioblastoma multiforme (GBM) cells, and Δ133p53α R273H in R273H mutant GBM cells. We used mRNA-sequencing to identify mutant Δ133p53α-specific target genes. We examined proliferation, invasion, DNA repair, apoptosis, and senescence regulation by WT and mutant Δ133p53α. All results were confirmed by siRNA knock-down. Finally, using TCGA data, we investigated the association of the mutant Δ133p53α-specific target genes to clinical outcome of GBM and low-grade glioma (LGG) patients. This study provides the first and most in-depth characterization of a mutant p53 isoform’s activities to date and demonstrate that mutant Δ133p53α R273H is an active contributor to glioblastoma carcinogenesis and response to treatment. Furthermore, by discovering the link between TP53 mutation and IL4I1/IDO1/AhR pathway, we show strong evidence of Δ133p53α R273H clinical relevance in mutant TP53 glioblastoma development and aggressiveness, and as a potential therapeutic target and biomarker.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

72 Samples

Download data: TXT

(Submitter supplied) Glioma cells and normal astrocytes were plated at low and high density to compare density-dependent gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

28 Samples

Download data: CEL

(Submitter supplied) The analysis presented here aims at exposing single-cell transcriptome profiles of Drosophila larval brain type II neural stem cells (NSCII) and of their intermediate neural progenitor (INP) cell progeny during normal development and upon brain tumour initiation using the brain tumour (brat) mutant model. We have used brains 24 hours after larval hatching (ALH), a developmental stage when brat INPs (b_INP) have transformed into brain tumour initiating cells, expressing aberrantly the self-renewal transcription factor Deadpan unlike their iINP control counterparts (c_iINP), but have not yet started to overproliferate. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL14121

7 Samples

Download data: DAT

(Submitter supplied) Exosomes generated from human bone marrow Mesenchymal Stem cells (MSC) and engineered to encapsulate different anti-Myc siRNAs (iExo-Myc) and scramble-siRNAs (iExo-Scr) were administered via retro-orbital injection to mice harboring late stage intracranial U87 tumor xenografts. Tumor growth and survival were monitored, and tumor xenografts were collected and transcriptionally profiled.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TSV

(Submitter supplied) Exosomes generated from human bone marrow Mesenchymal Stem cells (MSC) and engineered to encapsulate different anti-Myc siRNAs (iExo-Myc) and scramble-siRNAs (iExo-Scr) were administered via retro-orbital injection to mice harboring late stage intracranial U87 tumor xenografts. Tumor growth and survival were monitored, and tumor xenografts were collected and transcriptionally profiled. Next, we performed gene expression profiling analysis using data obtained from RNA-seq of U87 tumor xenografts collected at the endpoint of the survival study from 3 iExo-Myc#1 treated mice and 4 iExo-Scr#1 treated mice

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: TXT