|
| Status |
Public on Apr 15, 2020 |
| Title |
5560 native |
| Sample type |
RNA |
| |
|
| Source name |
primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy
|
| Organism |
Mus musculus |
| Characteristics |
cell type: primary lymphoma cells
treatment: native
genotype: Suv39h1 WT
phenotype: non-senescent
|
| Treatment protocol |
Freshly isolated lymphoma cells were retrovirally transduced by Bcl2 (MSCVpuro) and selected with Puromycin for 48h. These Myc;Bcl2 cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days
|
| Growth protocol |
Primary Emu-myc lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 4mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (20Gy) NIH 3T3 cells as feeder.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA from untreated or 5 days ADR treated Myc;Bcl2 lymphomas was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instruction.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MOE430 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Scanner G3000
|
| Description |
Primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice and retrovirally transduced by Bcl2 overexpression
|
| Data processing |
Affymetrix CEL files were imported into R (version 3.5.0) and processed by the RMA workflow implemented in the oligo package (median polish probe set summarization, RMA background correction, quantile normalization). Batch Effects were reduced by Empirical Bayes methods (ComBat) in the sva package. Treatment and phenotype were included as covariates in batch correction.
|
| |
|
| Submission date |
Jul 23, 2019 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Maja Milanovic |
| E-mail(s) |
maja.milanovic@charite.de
|
| Organization name |
Charite University Medicine, Berlin
|
| Department |
Hematology and Oncology
|
| Lab |
Clemens Schmitt
|
| Street address |
Augustenburgerplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE134753 |
Expression data from treatment-induced senescence in mouse Emu-myc B-cell lymphoma model. |
|
| Relations |
| Reanalysis of |
GSM937987 |
