|
| Status |
Public on Feb 12, 2021 |
| Title |
Panobinostat treatment, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
DIPG neurospheres, panobinostat treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HSJD-DIPG007
cell type: Diffuse intrinsic pontine glioma (DIPG) neurospheres
treatment: panobinostat
|
| Treatment protocol |
72 hours after incubation, cells were treated for 24 hours with DMSO, 0.6μM CBL0137, 20nM panobinostat and the combination of the two agents.
|
| Growth protocol |
HSJD-DIPG007 cells were cultured in DMEM/F12 and Neurobasal media (1:1) supplemented with HEPES, non-essential amino acids, antibiotic/antimycotic, pyruvate, glutamax, heparin, B27, human EGF, human FGF, PDGF-AA and PDGF-BB for 72 hours to form neurospheres.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy extraction kit (Qiagen; Cat No./ID: 74106) according to the manufacturer’s instruction.
|
| Label |
biotin
|
| Label protocol |
As per Affymetrix protocol
|
| |
|
| Hybridization protocol |
As per Affymetrix protocol
|
| Scan protocol |
As per Affymetrix protocol
|
| Data processing |
The probes from the Clariom D microarray were assigned to Ensembl Genes using custom chip definition file (CDF) clariomdhumanhsensgcdf (version 22.0.0) from (http://mbni.org/customcdf/22.0.0/ensg.download/clariomdhumanhsensgcdf_22.0.0.tar.gz) (PMID 16284200). The array data were analysed using Bioconductor/R andhe Robust MultiArray (RMA) pipeline (PMID 21070630), and batch effects were removed using the remove unwanted variation (ruv) R library and the RUVIII function (PMID 31114909) with one unwanted factor (k=1).
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Feb 12, 2021 |
| Contact name |
Chi Nam Ignatius Pang |
| E-mail(s) |
i.pang@unsw.edu.au
|
| Organization name |
The University of New South Wales
|
| Department |
The NSW Systems Biology Initiative
|
| Lab |
Wilkins Lab
|
| Street address |
School of Biotechnology and Biomolecular Sciences, UNSW Australia
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL28782 |
| Series (1) |
| GSE153441 |
Combination of CBL0137 and Panobinostat in DIPG |
|
