|
| Status |
Public on Dec 11, 2020 |
| Title |
9_Mo_d2 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: SHH-MB tumor cells from tumors of Atoh1-cre:SmoM2 mice at P12
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 |
MB1_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 |
GPL19057 |
| 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 |
SAMN16497345 |
| SRA |
SRX9326716 |
