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Sample GSM5920714 Query DataSets for GSM5920714
Status Public on Mar 04, 2024
Title P5
Sample type SRA
 
Source name Choroid plexus tumor
Organism Homo sapiens
Characteristics tissue: Chroid Plexus tumor tissue
subtype: Choroid plexus papilloma
Extracted molecule total RNA
Extraction protocol DNA was isolated with QIAMP DNA mini kit (QIAGEN). RNA was isolated using mirVana isolation kit (Invitrogen).
Library construction and sequencing were performed at the Beijing Genomics Institute (BGI), Hong Kong
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description transcript_level_raw_counts_kallisto.txt
Data processing Tools provided by Babraham bioinformatics group (FastQC v0.11.7, TrimGalore! v0.5.0) were used in quality control for both RRBS and RNA-seq fastq-files
The trimmed RRBS files were mapped using Bismark v0.19.1 followed by the differential methylation calling in regional level ( 1000 bp tiles) in R-enviroment (version 3.5.2) using methylKit v1.8.1. Only CpG-sites with at least 10 reads coverage were included.
The trimmed RNA-seq files were mapped using using kallisto v0.44.0
Genome_build: hg38 (UCSC)
Supplementary_files_format_and_content: txt-files that contain feature matrices for the samples: 1) methylation percentage matrix for the 1000 bp regions ("tiles") produced by methylKit (for region level differential methylation analysis) and 2) transcript-level raw count matrix from kallisto that is compatible with tximport and can be used to differential expression analysis in transcript level or gene level.
 
Submission date Feb 28, 2022
Last update date Mar 04, 2024
Contact name Kirsi Rautajoki
E-mail(s) kirsi.rautajoki@tuni.fi
Organization name Tampere university
Street address Arvo Ylpön katu 34
City Tampere
ZIP/Postal code 33520
Country Finland
 
Platform ID GPL11154
Series (1)
GSE197569 Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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