53411c45-70e8-4cbe-8540-628297734ca7 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006095 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:RNA-seq data for 54 Glioblastoma stem cell (GSC) lines. Fastq files of the strand-specific paired-end RNA-seq data are available.
| EGAD00001006195 | EGA
Project description:Single cell RNA-sequencing of glioblastoma stem cell (GSC) lines with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome using CellRanger.
| EGAD00001006804 | EGA
Project description:The DNA methylation profiles of Glioma Stem Cell (GSC) lines were investigated in order to find the stem cell signature associated to glioblastoma (GBM). This goal was achieved through the comparison of GSC methylation data with FFPE-GBM biopsies and human foetal Neural Stem Cell (NSC) lines profiles.
2013-03-08 | GSE41824 | GEO
Project description:RNA-seq data use in a study evaluating the effect of an PRMT5 inhibitor on GSC lines.
| EGAS00001004397 | EGA
Project description:The bromodomain and extra-terminal domain (BET) family consists of acetyllysine-binding proteins involved in many cancers, including glioblastoma multiforme. While the BET family activates transcription through binding to hyperacetylated histone H4 with simultaneous acetylation of K5 and K8 (H4K5acK8ac), so far epigenomic analysis of the BET family has mainly focused on H3K27ac, which is not their binding target. Here, we have examined the epigenomic profiles, including H4K5acK8ac and a BET family protein, BRD4, along with transcriptomics using a BET inhibitor, JQ1, in three human glial cell lines. We found that the expression of genes in which H4K5acK8ac is preferred over H3K27ac at promoters was mostly downregulated upon JQ1 in a glioblastoma stem cell (GSC) line. Knockdown of genes with the H4K5acK8ac-preferred promoters diminished the stemness of GSC. By defining super-enhancers (SEs) ranked by H4K5acK8ac, we found that 43% of the H4K5acK8ac-ranked SE were different from H3K27ac-ranked SE in GSC. CRISPR-Cas9-mediated deletion of the H4K5acK8ac-preferred SEs reduced the expression of associated genes including MYCN and NFIC in GSC and diminished its stemness. These results validate a novel strategy to identify genes involved in the regulation of glioblastoma stemness, through histone H4 hyperacetylation.
2023-07-23 | GSE178471 | GEO
Project description:Malignant glioblastoma (GBM) is a highly aggressive brain tumor with a dismal prognosis and limited therapeutic options. Genomic profiling of GBM samples in the TCGA database has identified four molecular subtypes (Proneural, Neural, Classical and Mesenchymal), which may arise from different glioblastoma stem-like cell (GSC) populations. In the present study, we identify two GSC populations that produce GBM tumors by subcutaneous and intracranial injection with identical histological features. Gene expression analysis revealed that xenografts of GSCs grown as spheroid cultures had a Classical molecular subtype similar to that of bulk tumor cells. In contrast xenografts of GSCs grown as adherent cultures on laminin-coated plates expressed a Mesenchymal gene signature. Adherent GSC-derived xenografts had high STAT3 and ANGPTL4 expression as well as enrichment for stem cell markers, transcriptional networks and pro-angiogenic markers characteristic of the Mesenchymal subtype. Examination of clinical samples from GBM patients showed that STAT3 expression was directly correlated with ANGPTL4 expression, and that increased expression of these genes correlated with poor patient survival and performance. A pharmacological STAT3 inhibitor abrogated STAT3 binding to the ANGPTL4 promoter and exhibited anticancer activity in vivo. Taken together, we identified two distinct GSC populations that produce histologically identical tumors but with very different gene expression patterns, and a STAT3/ ANGPTL4 pathway in glioblastoma that may serve as a target for therapeutic intervention. 2 samples of each variable were analyzed. Cells were cultured under normal adherent conditon (Bulk tumor cells), non-adherent plates with stem cell medium (Sp-GSC) or laminin-coated plates with stem cell medium (Ad-GSC). Xenografts were generated in NSG mice by subcutaneous inoculation.
2015-07-01 | E-GEOD-65576 | biostudies-arrayexpress
Project description:Using induced pluripotent stem cell (iPSC) technology, we reprogrammed GBM derived cells (GBM-DCs) into embryonic-like cells termed as induced core-GSCs (ic-GSCs). The aim of this experiment was to characterize the transcriptomic profile of ic-GSCs using RNA-seq. For this experiment, we selected three biological replicates of GBM-DCs (GBM-DC1, GBM-DC2 and GBM-DC3) and three independent clonal lines of ic-GSCs (ic-GSC#1, ic-GSC#3 and ic-GSC#7).
2022-05-11 | E-MTAB-10977 | biostudies-arrayexpress
Project description:The DNA methylation profiles of Glioma Stem Cell (GSC) lines were investigated in order to find the stem cell signature associated to glioblastoma (GBM). This goal was achieved through the comparison of GSC methylation data with FFPE-GBM biopsies and human foetal Neural Stem Cell (NSC) lines profiles. GSC lines: 3 (GBM2, G144, G166). FFPE-GBM biopsy pool: FFPE-GBM pool: 1 pool from 5 GBM biopsies. Human foetal NSC lines: 2 (CB660 from forebrain; CB660SP form spinal cord). Methylated DNA from each sample was enriched with the immunoprecipitation method using 5-methylcytosine antibody (Eurogentec). Immunoprecipitated DNA (IP-DNA) and total DNA were labeled and hybridized on Agilent Human CpG Island ChIP-on-Chip Microarray 244K. IP-DNA were labeled with Cy5 while the matching total DNA were labeled with Cy3.
2013-03-08 | E-GEOD-41824 | biostudies-arrayexpress
Project description:WGS data for 20 Glioblastoma stem cell (GSC) lines and matched blood samples. Fastq files are available.
For 10 GSC samples and the 10 matched blood samples the reads are on 3 fastq files per sample
| EGAD00001006488 | EGA
Project description:Glioblastoma multiforme (GBM), the most common and malignant type of glioma, is characterized by a poor prognosis and the lack of an effective treatment, which are due to a small sub-population of cells with stem-like properties, termed glioma stem cells (GSCs). The term M-bM-^@M-^\multiformeM-bM-^@M-^] describes the histological feature of this tumor, i.e. the cellular and morphological heterogeneity. At the molecular level multiple layers of alterations may reflect this heterogeneity providing together the driving force of tumor initiation and development. In order to decipher the common M-bM-^@M-^\signatureM-bM-^@M-^] of the ancestral GSC population, we examined 5 already characterized GSC lines evaluating their copy number alterations using a genome-wide approach. Genomic DNA was isolated from 5 Glioma Stem Cell (GSC) lines. Each sample was labeled with Cy3 dye and then hybridized against the same commercial reference DNA labeled in Cy5.
2013-03-08 | E-GEOD-41875 | biostudies-arrayexpress