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Sample GSM777566 Query DataSets for GSM777566
Status Public on Aug 18, 2011
Title CPG-stimulated B-CLL_mutated repl 8
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 8 of 8
251485057173_1_1_G48_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 0.227815172
2 1.216126793
3 1.298257081
4 1.078562826
5 1.173759601
6 1.001309939
7 1.281673438
8 0.689525136
9 0.383239629
10 0.460409979
11 0.034385698
12 1.280785413
13 -0.45349137
14 -0.466908407
15 0.938893113
16 1.810016184
17 0.659744039
18 0.63950125
19 -0.07294516
20 0.494186704

Total number of rows: 45015

Table truncated, full table size 797 Kbytes.




Supplementary file Size Download File type/resource
GSM777566_251485057173_1_1_G48_CpG.txt.gz 16.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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