|
| Status |
Public on Apr 25, 2024 |
| Title |
560_hBim_S6 |
| Sample type |
SRA |
| |
|
| Source name |
Eu-Myc mouse lymphoma
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Eu-Myc mouse lymphoma
cell line: 560
cell type: lymphoma
genotype: WT
treatment: S63845
|
| Treatment protocol |
Cells were pretreated for 15 min with caspase inhibitor QVD-O-Ph, followed by DMSO, S63845 (300 nM), diABZI (100 nM) or both S63845 and diABZI for 24 h.
|
| Growth protocol |
Cels were maintained in FMA media (DME Kelso, 10% heat-inactivated FBS, 100 uM L-asparagine, 50 uM beta-mercaptoethanol) at 37C with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell pellets were resuspended in TRIzol reagent (Invitrogen) and RNA extracted according to the manufacturer's instructions.
RNA libraries were constructed from 200 ng of RNA per sample using the TruSeq RNA Library Prep Kit v2 (Illumina), according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
B02_560 hBim S6
|
| Data processing |
Data was analysed on the Galaxy Australia server
Sequencing reads were aligned to mm10 using hisat2 v2.2.1.
Read counts were obtained using featureCounts from subread v2.0.3.
Read filtering, normalisation and differential expression analysis was performed using limma-voom v3.50.1. Genes that did not meet a minimum expression level of CPM > 0.5 in at least 2 samples were filtered out. Normalisation performed using the TMM method.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes limma-voom filtered and normalised read counts for each sample
|
| |
|
| Submission date |
Mar 12, 2024 |
| Last update date |
Apr 25, 2024 |
| Contact name |
Sarah T Diepstraten |
| E-mail(s) |
diepstraten.s@wehi.edu.au
|
| Organization name |
The Walter and Eliza Hall Institute
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE261373 |
Putting the STING back into BH3-mimetic drugs for TP53 mutant blood cancers |
|
| Relations |
| BioSample |
SAMN40411875 |
| SRA |
SRX23907345 |
