|
| 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
SRT_F31_0009_P01_V11
|
| 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 |
| E-mail(s) |
a.canalda@nencki.edu.pl
|
| 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 |
|
| Relations |
| BioSample |
SAMN19115398 |
| SRA |
SRX10852924 |
