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Sample GSM5291628 Query DataSets for GSM5291628
Status Public on Apr 15, 2022
Title U87 siCTRL RNAseq IDHmut rep1
Sample type SRA
Source name U87 siCTRL RNAseq IDHmut
Organism Homo sapiens
Characteristics cell type: U87 human glioma cell line
tissue: brain
genotype: IDH1 knockdown
sample type: IDH1 mutant-U-87 isogenic cell line
transfection: REST-targeting siRNA
Extracted molecule polyA RNA
Extraction protocol RNA libraries were prepared using KAPA Stranded mRNAseq protocol
DNA libraries for ChIPseq were prepared using Qiaseq Ultra Low Input protocol
Library strategy ChIP-Seq
Library source transcriptomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Description data_norm_DESeq2_1.xlsx
Data processing In the RNAseq primary analysis, Illumina-specific adapters, low-quality 5’ and 3’ bases and short reads were removed in the FASTQ files using Trimmomatic tool.
RNA sequencing reads were aligned to a reference human genome sequence (hg38) using the STAR aligner.
Duplicates were identified and marked using Picard Tools and the resulting RNAseq mapped reads were summarized and counted by gene using HTseq, in paired-end mode, reverse-stranded mode and considering only reads with MAPQ values of 3 or higher and primary aligment.
Low-expressed genes were prefiltered and an a analysis of differentially expressed genes was performed using DESeq2.
In the ChIPseq primary analysis, reads with phred values >30 were retained for downstream analysis.
PCR duplicates were marked and removed using Picard Tools and the resulting reads were mapped to the human genome with the BWA-MEM algorithm.
Peaks were called with MACS2 software using default parameters, and secondary peak analysis was performed with the R libraries ChipSeeker and clusterProfiler.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 normalized abundance measurements ouput
Supplementary_files_format_and_content: MACS2 narrow peaks files
Submission date May 12, 2021
Last update date Apr 15, 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
Platform ID GPL18460
Series (1)
GSE174308 REST transcription factor holds the balance between the invasion and cell differentiation in IDH-mutant and IDH-wild type gliomas
BioSample SAMN19115398
SRA SRX10852924

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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