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Sample GSM1083878 Query DataSets for GSM1083878
Status Public on Jul 04, 2013
Title lymphoma_4936_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 GSM3966993

Data table header descriptions
VALUE Normalized log2 signal intensity

Data table
1415670_at 8.505
1415671_at 8.59841
1415672_at 10.631
1415673_at 8.7407
1415674_a_at 8.28779
1415675_at 8.18286
1415676_a_at 9.9241
1415677_at 7.09055
1415678_at 9.80354
1415679_at 9.81295
1415680_at 8.83005
1415681_at 9.33061
1415682_at 7.51174
1415683_at 9.72198
1415684_at 7.3494
1415685_at 8.18512
1415686_at 8.28069
1415687_a_at 10.752
1415688_at 9.95832
1415689_s_at 7.64044

Total number of rows: 45101

Table truncated, full table size 850 Kbytes.

Supplementary file Size Download File type/resource
GSM1083878_M9.CEL.gz 2.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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