|
| Status |
Public on Dec 26, 2018 |
| Title |
HSR-RNA-GBM1+VitC-RNA-2 |
| Sample type |
SRA |
| |
|
| Source name |
HSR-GBM1 glioblastoma cells cultured with vitaminC replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line derived from human glioblastoma
cell line: HSR-GBM1
cell-subtype: astrocytoma
cell type: Glioblastoma multiforme
|
| Treatment protocol |
HSR-GBM1 cells were cultured in the presence of 0.5 μM of 5-azacytidine (Sigma-Aldrich) for 48 hours or 100 μg/mL of Vitamin C (L-ascorbic acid, Sigma-Aldrich) for 72 hours. Culture media was changed every 24 hours.
|
| Growth protocol |
HSR-GBM1 cells were cultured as neurospheres on ultra-low attachment plates (Sigma) in Dulbecco's Modified Eagle Medium /Nutrient Mixture (DMEM/F-12) Media (Gibco) containing 2% StemPro neural supplement (Invitrogen Life Technologies), 20 ng/ml basic fibroblast growth factor (bFGF; Millipore) and 20 ng/ml epidermal growth factor (EGF; Millipore) at 37 °C, 5% CO2 and 95% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total genomic RNA were extracted from cultured cell pellets using the RNeasy and QiaShredder Kits (Qiagen) according to manufacturer’s protocols . The DNA samples were treated with 3 μL of RNase solution (Qiagen) and Proteinase K Solution (20 μg/μL; Qiagen) at 65 °C for 10 minutes.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer.
The Illumina bcl2fastq 2.19.0.316 pipeline was used to generate the sequence data.
Sequences were mapping to the human genome hg38 using STAR software 2.5.3a.
Porvides uniquely mapped reads in counts for each gene by the featureCounts function in Rsubread package (1.26.0) using the inbuilt annotation hg38.
Identification of differentially expressed genes by edgeR package (3.16.5).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing read counts values of each gene for each sample; csv file containing statistical results by edgeR package.
|
| |
|
| Submission date |
May 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Justin C St. John |
| E-mail(s) |
justin.stjohn@hudson.org.au
|
| Phone |
+61399024749
|
| Organization name |
Hudson Institute of Medical Research
|
| Department |
Centre for Genetic Diseases
|
| Lab |
Mitochondrial Genetics
|
| Street address |
27-31 Wright St
|
| City |
Clayton |
| State/province |
Vic |
| ZIP/Postal code |
3168 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE98692 |
Impact of DNA demethylation agents (5-azacytidine or vitamin C) on gene expression in glioblastoma HSR-GBM1 cells |
| GSE98693 |
Induced DNA demethylation, genome instability and transcription |
|
| Relations |
| BioSample |
SAMN06920683 |
| SRA |
SRX2792539 |
