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Sample GSM777561 Query DataSets for GSM777561
Status Public on Aug 18, 2011
Title CPG-stimulated B-CLL_mutated repl 3
Sample type RNA
 
Channel 1
Source name CPG stimulated purified cell of CLL mutated
Organism Homo sapiens
Characteristics cell type: purified CLL cells
Extracted molecule total RNA
Extraction protocol CLL cells were purified by negative selection using anti-CD3, anti-CD14 and anti-CD16 mouse monoclonal antibodies and Dynabeads coated with a pan anti-mouse IgG antibody. The purity of the CLL cells after negative selection was monitored by flow-cytometry and the percentage of CD5+/CD19+ cells exceeded 98% for each sample. CLL cells were resuspended in RPMI complete medium at a density of 2 × 105 and stimulated with 7.5 μg/ml complete phosphorothioate CpG ODN oligonucleotide 2006 (5′-TCGTCGTTTTGTCGTTTTGTCGTT-3′) or left unstimulated for 18 h.Total RNA was extracted according to TRIZOL reagent protocol
Label Cy5
Label protocol Total RNA was labelled according to Ambion protocol. 825 ng of Cy3-labeled reference aRNA (according to Agilent protocol)
 
Channel 2
Source name reference
Organism Homo sapiens
Characteristics sample origin: pooled normal PB B cells of healthy donors
Extracted molecule total RNA
Extraction protocol CLL cells were purified by negative selection using anti-CD3, anti-CD14 and anti-CD16 mouse monoclonal antibodies and Dynabeads coated with a pan anti-mouse IgG antibody. The purity of the CLL cells after negative selection was monitored by flow-cytometry and the percentage of CD5+/CD19+ cells exceeded 98% for each sample. CLL cells were resuspended in RPMI complete medium at a density of 2 × 105 and stimulated with 7.5 μg/ml complete phosphorothioate CpG ODN oligonucleotide 2006 (5′-TCGTCGTTTTGTCGTTTTGTCGTT-3′) or left unstimulated for 18 h.Total RNA was extracted according to TRIZOL reagent protocol
Label Cy3
Label protocol Total RNA was labelled according to Ambion protocol. 825 ng of Cy3-labeled reference aRNA (according to Agilent protocol)
 
 
Hybridization protocol The Hybridization was performed acording to Ambion protocol
Scan protocol Slides were analysed by Agilent Microarray Scanner G2565AA
Description Biological replicate 3 of 8
251485057173_1_1_G42_CpG
Data processing Background subtraction method: Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.Whithin Normalization method: loess. Between Normalization method: quantile
 
Submission date Aug 12, 2011
Last update date Aug 18, 2011
Contact name daniela marconi
E-mail(s) daniela.marconi@gmail.com
Organization name CRO AVIANO
Street address Via franco Gallini 2
City Aviano
ZIP/Postal code 33081
Country Italy
 
Platform ID GPL4133
Series (2)
GSE30107 miRNA and mRNA expression profile of CLL cells
GSE31360 CPG stimulation for Gene Expression of mutated B-CLL

Data table header descriptions
ID_REF
VALUE quantile normalized loess log2 red/green signal

Data table
ID_REF VALUE
1 0.217562051
2 1.291157327
3 0.858356621
4 0.903842466
5 0.786978675
6 0.771774538
7 0.616762469
8 0.905802834
9 0.859893866
10 0.729758711
11 0.689853042
12 1.509635706
13 0.820949839
14 -0.702291642
15 1.021146448
16 0.048154662
17 0.358737168
18 1.214117292
19 1.101176216
20 0.618909586

Total number of rows: 45015

Table truncated, full table size 797 Kbytes.




Supplementary file Size Download File type/resource
GSM777561_251485057173_1_1_G42_CpG.txt.gz 16.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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