|
Status |
Public on Mar 04, 2024 |
Title |
P1 |
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 |
|