|
|
| Status |
Public on Jul 19, 2016 |
| Title |
U-87_22-3-15 |
| Sample type |
SRA |
| |
|
| Source name |
Glioblastoma cultured cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain tumor cell line
cell line: U-87
treatment: Not treated
|
| Treatment protocol |
Cells were counted and plated in new 150 mm Petri dishes one day prior to the treatment. The following day, the media was removed and replaced with fresh medium with or without 1 μM of 5'-Aza-2'-deoxycytidine (Decitabine, Enco diagnostics, AdooQ bioscience). After incubation with Decitabine for 72 hours, the cells were harvested, counted and prepared for RNA sequencing.
|
| Growth protocol |
Three human Glioblastoma cell lines, U-87, T98G and LNT-229 (obtained from the ATCC) were maintained in DMEM supplemented with 10% FBS, 1% L-glutamine, 1% Na-pyruvate, 0.1 mg/ml streptomycin and 100 μ/ml penicillin and 0.1% HEPES. The cells were kept in 5% CO2 humidified incubator at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from between 1 to 2*106 GBM cells, using the Total RNA Purification Plus kit (Norgen biotec) as per the kit instructions. The isolated total RNA was quantified using Qubit 2.0 machine (Invitrogen) before the sequencing library preparation. The mRNA population in each sample was enriched by removing ribosomal RNA (rRNA) using the Epicenter ScriptSeq Complete kit (human, Illumina) as per the kit instructions.
The experiment was performed by Illumina HiSeq 2500 in 50 base pair single read mode in the Technion Genome Center. The RNA-seq reads were mapped to the GRCh38 genome using TopHat version 2.0.13. Only uniquely mapped reads were counted in the analysis, using the HTSeq-count package version 0.6.1 with ‘union’ mode. The counts normalization and the differential expression analysis were done using the DESeq2 package version 1.8.1.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The experiment was performed by Illumina HiSeq 2500 in 50 base pair single read mode
The RNA-seq reads were mapped to the GRCh38 genome using TopHat version 2.0.13
Only uniquely mapped reads were counted in the analysis, using the HTSeq-count package version 0.6.1 with ‘union’ mode
The counts normalization and the differential expression analysis were done using the DESeq2 package version 1.8.1
Genome_build: GRCh38 genome
Supplementary_files_format_and_content: Excel file includes normalized counts
|
| |
|
| Submission date |
Apr 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Arie Admon |
| E-mail(s) |
admon@tx.technion.ac.il
|
| Organization name |
Technion - Israel Institute of Technology, Haifa, Israel
|
| Department |
Department of Biology
|
| Street address |
Kiryat Technion- Emerson building
|
| City |
Haifa |
| State/province |
select a state |
| ZIP/Postal code |
320000 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE80137 |
HLA peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy |
|
| Relations |
| BioSample |
SAMN04632410 |
| SRA |
SRX1689928 |
