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Series GSE206357 Query DataSets for GSE206357
Status Public on Mar 01, 2023
Title Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Glioblastoma (GBM, WHO grade IV) is an aggressive, primary brain tumor. Despite gross surgery and forceful radio- and chemotherapy, survival of GBM patients did not improve over decades. Several studies reported transcription deregulation in GBMs but regulatory mechanisms driving overexpression of GBM-specific genes remain largely unknown. Transcription in open chromatin regions is directed by transcription factors (TFs) that bind to specific motifs, recruit co-activators/repressors and a transcriptional machinery. Identification of GBM-related TFs-gene regulatory networks may reveal new, targetable mechanisms of gliomagenesis.
Overall design We predicted TFs-regulated networks in GBMs in silico and intersected them with putative TF binding sites identified in accessible chromatin in human glioma cells and GBMs. The Cancer Genome Atlas and gliomaAtlas datasets (DNA methylation, H3K27 acetylation, transcriptomic profiles) were explored to elucidate TFs-gene regulatory networks and effects of the epigenetic background
Contributor(s) Roura A, Szadkowska P, Poleszak K, Stepniak K, Dabrowski MJ, Ellert-Miklaszewska A, Wojnicki K, Ciechomska I, Stepniak K, Kaminska B, Wojtas B
Citation(s) 36850002
Submission date Jun 17, 2022
Last update date Jun 14, 2023
Contact name Adria-Jaume Roura
Organization name Nencki Institute of Experimental Biology, Polish Academy of Sciences
Street address Ludwika Pasteura 3
City Warsaw
ZIP/Postal code 02-093
Country Poland
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (6)
GSM6252555 LN18 glioma cell line RNAseq rep1
GSM6252556 LN18 glioma cell line RNAseq rep2
GSM6252557 LN229 glioma cell line RNAseq rep1
BioProject PRJNA850386

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Supplementary file Size Download File type/resource
GSE206357_DESeq2_LN18_LN229_RNAseq_raw.counts.txt.gz 4.9 Mb (ftp)(http) TXT
GSE206357_RAW.tar 780.0 Kb (http)(custom) TAR (of BROADPEAK)
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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