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Sample GSM3966990 Query DataSets for GSM3966990
Status Public on Apr 15, 2020
Title 9250 5d ADR
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: 5d ADR
genotype: Suv39h1-
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 GSM1083875

Data table header descriptions
ID_REF
VALUE normalized log2 signal intensity

Data table
ID_REF VALUE
1415670_at 8.359492339
1415671_at 8.887515113
1415672_at 10.50982677
1415673_at 8.480763632
1415674_a_at 9.085257594
1415675_at 8.523335343
1415676_a_at 10.3711011
1415677_at 6.665769556
1415678_at 9.172731162
1415679_at 10.06691317
1415680_at 9.511818858
1415681_at 9.813266317
1415682_at 8.004035217
1415683_at 10.17753406
1415684_at 7.270172133
1415685_at 9.244210274
1415686_at 8.279005897
1415687_a_at 11.31035208
1415688_at 9.619641783
1415689_s_at 7.981591803

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM3966990_M6.CEL.gz 2.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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