|
| Status |
Public on Feb 28, 2017 |
| Title |
PDGFB K27M T4 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse tumor derived from PDGF K27M Neural Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse tumor derived from PDGF K27M Neural Stem Cells
genotype: K27M
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from tumours isolated from the mice were extracted using Rneasy plus kit (Qiagen).
500 ng of total RNA was used to make the library of polyA RNA using TruSeq RNA sample prep kit (Illumina) accordig to the protocol provided by the supplier. The libraries were sequenced using Illumina HiSeq2500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
treatment: Untreated
|
| Data processing |
After removal of Illumina adapter sequences with skewer, RNA-seq reads were mapped to the mouse genome (UCSC mm10) assembly using STAR with default parameters. The release vM8 of mouse transcript annotations were downloaded from the Gencode project (http://www.gencodegenes.org) and read counts per gene were computed using the featureCounts program.
Genome_build: mm10
Supplementary_files_format_and_content: Table of gene read counts made using featureCounts and Gencode vM8 annotations
|
| |
|
| Submission date |
Aug 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Faizaan Mohammad |
| E-mail(s) |
faizaan.mohammad@bric.ku.dk
|
| Organization name |
BRIC
|
| Street address |
Ole Maaloøs vej 5 Fourth Floor
|
| City |
Copenhagen |
| State/province |
Choose A State |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE85388 |
EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas [RNA-Seq mouse tumors] |
| GSE85390 |
EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas |
|
| Relations |
| BioSample |
SAMN05553009 |
| SRA |
SRX2010529 |
