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Sample GSM1083874 Query DataSets for GSM1083874
Status Public on Jul 04, 2013
Title lymphoma_9250_nt
Sample type RNA
Source name Primary lymphoma cells, isolated from lymph nodes of Emu-myc,Suv39h1-/- mice and retrovirally transduced by Bcl2, untreated
Organism Mus musculus
Characteristics genotype: Emu-myc;Suv39h1-/-
transduction: Bcl2
cell type: primary lymphoma cells from lymph nodes
treatment: none
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;Suv39h1-/- 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 instructions.
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; Suv39h1-/- mice with palpable lymphadenopathy.
Data processing Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).
Submission date Feb 15, 2013
Last update date Jul 23, 2019
Contact name Maja Milanovic
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)
GSE44355 Expression data from Adriamycin-treated Emu-myc; Suv39h1-/- B-cell lymphoma
Reanalyzed by GSM3966989

Data table header descriptions
VALUE Normalized log2 signal intensity

Data table
1415670_at 8.59306
1415671_at 8.98442
1415672_at 10.522
1415673_at 8.98557
1415674_a_at 8.91965
1415675_at 8.36051
1415676_a_at 10.2943
1415677_at 7.50773
1415678_at 9.26397
1415679_at 9.92355
1415680_at 9.08941
1415681_at 9.36189
1415682_at 7.90115
1415683_at 10.1349
1415684_at 7.41761
1415685_at 8.60519
1415686_at 8.02118
1415687_a_at 10.8248
1415688_at 9.5701
1415689_s_at 7.31217

Total number of rows: 45101

Table truncated, full table size 849 Kbytes.

Supplementary file Size Download File type/resource
GSM1083874_M5.CEL.gz 2.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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