|
| Status |
Public on Feb 28, 2017 |
| Title |
PDGFB K27M EPZ III |
| Sample type |
SRA |
| |
|
| Source name |
PDGF Neural Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: PDGF Neural Stem Cells
genotype: K27M
|
| Treatment protocol |
The cells were treated with either DMSO or Ezh2 inhibitor (EPZ6438, 3 uM) for 12 days.
|
| Growth protocol |
Mouse cells were cultured on poly-D-lysine (PDL, Sigma) and laminin (Sigma) coated plates in neural stem cell medium (50% DMEM-F12, 50% neurobasal medium, N2 and B27 supplements, sodium pyruvate, glutamax, HEPES, β−mercaptoethanol, non-essential amino acids, bovine serum albumin, heparin, 100U/ml penicillin, 100 μg/ml streptomycin, human recombinant epidermal and basic fibroblast growth factors).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from in vitro cultured cells 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: EPZ
replicate: III
|
| Data processing |
Mouse transcript annotation version GRCm38.79 was downloaded from the Ensembl database (http://www.ensembl.org). Mapping and transcript pseudo-quantification were preformed using kallisto. Differential expression analysis was performed using sleuth according to the software manual.
Genome_build: mm10
Supplementary_files_format_and_content: Differential analysis results using kallisto and sleuth
|
| |
|
| 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) |
| GSE85385 |
EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas [RNA-Seq - mouse cell lines] |
| GSE85390 |
EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas |
|
| Relations |
| BioSample |
SAMN05552988 |
| SRA |
SRX2010409 |
