NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1083876 Query DataSets for GSM1083876
Status Public on Jul 04, 2013
Title lymphoma_1032_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
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)
GSE44355 Expression data from Adriamycin-treated Emu-myc; Suv39h1-/- B-cell lymphoma
Relations
Reanalyzed by GSM3966991

Data table header descriptions
ID_REF
VALUE Normalized log2 signal intensity

Data table
ID_REF VALUE
1415670_at 8.44901
1415671_at 10.2514
1415672_at 10.8638
1415673_at 9.49426
1415674_a_at 8.96869
1415675_at 8.34769
1415676_a_at 10.2582
1415677_at 9.40172
1415678_at 9.01206
1415679_at 10.1114
1415680_at 8.48915
1415681_at 9.04629
1415682_at 7.64727
1415683_at 10.2835
1415684_at 7.84971
1415685_at 8.52676
1415686_at 8.42132
1415687_a_at 11.7713
1415688_at 9.43687
1415689_s_at 7.59255

Total number of rows: 45101

Table truncated, full table size 850 Kbytes.




Supplementary file Size Download File type/resource
GSM1083876_M7.CEL.gz 2.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap