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Series GSE174308 Query DataSets for GSE174308
Status Public on Apr 15, 2022
Title REST transcription factor holds the balance between the invasion and cell differentiation in IDH-mutant and IDH-wild type gliomas
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Glioblastoma is the deadliest brain tumor with median survival of 15 months due to diffusive growth and lack of efficient therapy. Recurrent mutations in genes coding for isocitrate dehydrogenases (IDH) 1 or 2 cause to a change in function of the enzymes, resulting in production of 2-hydroxyglutarate, which leads to DNA hypermethylation phenotype, affecting transcription activators/repressors binding to DNA and gene expression. REST is a canonical repressor of neuronal genes in non-neuronal cells, whose levels differ between IDH wt and mut gliomas and whose expression levels correlate with the patients’ survival probability.
Overall design IDH1 mutant-U-87 Isogenic Cell Line and malignant glioma U-87 MG were used in the experiments. For each cell line, REST-chromatin immunoprecipitation was performed twice, followed by sequencing and position weight matrix (PWM) analysis. Total RNA was extracted from U-87 MG and IDH1 mutant-U-87 isogenic cell lines that had not been treated, had control siRNA transfected, and had REST-targeting siRNA transfected. Following the construction and sequencing of mRNA sequencing libraries, differential analysis between REST knockdown and control samples was performed.
Contributor(s) Perycz M, Jardanowska M, Roura AJ, Stepniak K, Gielniewski B, Dabrowski MJ, Kaminska B, Wojtas B
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Submission date May 12, 2021
Last update date Apr 16, 2022
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 (26)
GSM5291618 U87 input ChIPseq IDH1wt rep1
GSM5291619 U87 input ChIPseq IDH1mut rep1
GSM5291620 U87 REST ChIPseq IDH1wt rep1
BioProject PRJNA729272
SRA SRP319405

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Supplementary file Size Download File type/resource
GSE174308_RAW.tar 320.0 Kb (http)(custom) TAR (of NARROWPEAK)
GSE174308_data_norm_DESeq2_1.xlsx 5.2 Mb (ftp)(http) XLSX
GSE174308_data_norm_DESeq2_2.xlsx 3.2 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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