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Sample GSM4844199 Query DataSets for GSM4844199
Status Public on Dec 11, 2020
Title 13_Do_d2
Sample type SRA
 
Source name cell line
Organism Homo sapiens
Characteristics cell type: Group 3 medulloblastoma cells
culture: Co-culture
Treatment protocol For co-culture experiments 30 mm Millicell cell culture inserts with hydrophilic PTFE membranes (0.4 µm pore size) were used (Millipore, Merck).
Growth protocol All cells were maintained at 37°C and 5% CO2 in DMEM/F-12 medium containing B-27 and N-2 supplements (Gibco, Thermo Fisher Scientific), 20 ng/mL of recombinant murine EGF and basic fibroblast growth factor (bFGF) (PeproTech Germany), and 1% penicillin/streptomycin (Gibco). For co-culture experiments 30 mm Millicell cell culture inserts with hydrophilic PTFE membranes (0.4 µm pore size) were used (Millipore, Merck).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy mini Kit (Qiagen) as specified by the manufacturer.
Sequencing libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer's guidelines.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description D341_txi_abundance.txt
Data processing After explorative quality control with FastQC (v0.11.8) and MultiQC (v1.7), we used Salmon (v0.14.1) for pseudo-alignment and quantification of the samples to the human and mouse transcriptomes (downloaded from Ensembl, release 94). Default parameters were used.
Further analyses were performed in R. We employed the Bioconductor package tximport (v1.10.1) to summarize transcript-level estimates computed by Salmon for a gene-level analysis.
To find differentially expressed genes, we used the package DESeq2 (v1.22.2) and tested for co-culture effects. In order to control for possible batch effects, we included this variable in the formula definition of DESeq2 (i.e. ~batch + condition).
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: Supplementary file abundances.tar.gz contains three tab-separated text files (one for each different cell line: D341, MB1 and OLI) with transcript-level abundances for each sample, generated as in the preprocessing steps above.
 
Submission date Oct 21, 2020
Last update date Dec 11, 2020
Contact name Kornelius Kerl
E-mail(s) kornelius.kerl@ukmuenster.de
Organization name University Children's Hospital Münster
Department Department of Pediatric Hematology and Oncology
Street address Albert-Schweitzer-Campus 1
City Münster
ZIP/Postal code 48149
Country Germany
 
Platform ID GPL18573
Series (2)
GSE159763 (bulk RNAseq) An extracellular vesicle-related gene expression signature identifies high-risk patients in medulloblastoma
GSE160003 An extracellular vesicle-related gene expression signature identifies high-risk patients in medulloblastoma
Relations
BioSample SAMN16497369
SRA SRX9326720

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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