|
| Status |
Public on Mar 22, 2024 |
| Title |
LNZ308 24h B |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
cell line: LNZ308
cell type: cell line
genotype: p53 del, PTEN mut, p16 wt, p14ARF wt
treatment: 24h AZD6738
|
| Treatment protocol |
LN229 cells were treated with 1.6 µM AZD6738, LNZ308 cells were treated with 3.5 µM AZD6738; DMSO was used as vehicle and applied in equal amounts as AZD6738
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit; enrichment of the mRNA fraction using polyA capture from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB)
NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (NEB)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
21023a020_01_S115
|
| Data processing |
To align the reads to the GRCh38 we used STAR v2.7.3a
alignment quality was analyzed using ngs-bits
Normalized read counts for all genes were obtained using Subread (v2.0.0) and edgeR (v3.26.6)
Lastly we used R package “DESeq2”
Assembly: GRCh38
Supplementary files format and content: count file matrix
|
| |
|
| Submission date |
Apr 13, 2023 |
| Last update date |
Mar 22, 2024 |
| Contact name |
Bianca Walter |
| E-mail(s) |
bianca.walter@uni-tuebingen.de
|
| Phone |
070712982043
|
| Organization name |
Hertie Institut für klinische Hirnforschung
|
| Street address |
Otfried-Müller-Str. 27
|
| City |
Tübingen |
| State/province |
Deutschland |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE229614 |
Functionally-instructed modifiers of response to ATR inhibition in experimental glioma |
|
| Relations |
| SRA |
SRX19951907 |
| BioSample |
SAMN34165117 |
