|
| Status |
Public on Jul 19, 2022 |
| Title |
DAXX KO cells, Etoposide treated, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
U87 glioblastoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87 glioblastoma cells
genotype: ATRX KO
treatment: etoposide
replicate: 2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer’s instructions. RNA was treated with Turbo DNA-free kit (life technologies) and quality checked with TapeStation (Agilent).
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DAXX.KO.trt.2
DAXX KO cells, Etoposide treated, replicate 2
|
| Data processing |
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene
|
| |
|
| Submission date |
Oct 22, 2021 |
| Last update date |
Jul 19, 2022 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
[email protected]
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE186440 |
DAXX-ATRX-H3.3 Regulation of p53 Chromatin Binding and DNA Damage Response [RNA-Seq] |
| GSE186443 |
DAXX-ATRX-H3.3 Regulation of p53 Chromatin Binding and DNA Damage Response |
|
| Relations |
| BioSample |
SAMN22513031 |
| SRA |
SRX12743662 |
