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Sample GSM96135 Query DataSets for GSM96135
Status Public on Feb 25, 2006
Title 32NM CLL vs reference
Sample type RNA
 
Channel 1
Source name RNA REFERENCE
Organism Homo sapiens
Characteristics Mix of equal amount of total RNAs from our cohort was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment.
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 32NM
Organism Homo sapiens
Characteristics CLL case with unmutated IgVH gene
Extracted molecule total RNA
Label cy5
 
 
Description For all 29 specimens, fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo alto, CA, USA) according to the manufacturer’s instructions. Amplified cRNA of each patient was labelled with cyanine 5-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Mix of equal amount of total RNAs from our cohort was used as reference control in all microarray gene-profiling experiments. Amplified reference cRNA was labelled with cyanine 3-CTP (Perkin-Elmer, NEN Life Science, Boston, MA, USA) in each experiment. Moreover, cRNA products were purified using RNeasy columns (Qiagen). 1 g of Cy5-labelled cRNA was mixed with the same amount of Cy3-labelled reference cRNA and then mixed cRNAs were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized on Agilent Human 1A Oligo Microarray, ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features).33 After hybridization for 17 h at 60°C, slides were washed according to Agilent SSC protocol instructions and then scanned using a confocal laser scanner (Agilent Technologies).
Data processing linear and lowess normalization (Agilent settings)
 
Submission date Feb 08, 2006
Last update date Feb 24, 2006
Contact name Rossana Maffei
E-mail(s) rossana.maffei@unimore.it
Phone +39 059 4222715
Organization name University of Modena and Reggio Emilia
Department Dept of Hematology and Oncology
Lab Lab of Molecular Hematology
Street address Via del Pozzo 71
City Modena
State/province Modena
ZIP/Postal code 41100
Country Italy
 
Platform ID GPL885
Series (1)
GSE4207 B-cell chronic lymphocytic leukemia gene expression profiles

Data table header descriptions
ID_REF
VALUE log10 ratio
gProcessedSignal dye-normalized cy3 signal
rProcessedSignal dye-normalized cy5 signal

Data table
ID_REF VALUE gProcessedSignal rProcessedSignal
1 -0.73 3847 714
2 0.00 20 36
3 0.01 164 169
4 0.19 4853 7516
5 -0.03 1225 1154
7 -1.06 3264 284
8 -0.04 3380 3074
9 0.02 1890 1965
11 0.07 245 291
13 0.08 218 260
14 -1.05 3466 309
15 0.03 6389 6840
16 0.02 810 856
17 -0.02 37 36
21 -1.09 3335 272
23 0.02 238 250
25 -0.12 234 178
26 0.01 355 361
28 -1.04 3588 328
29 0.10 2829 3560

Total number of rows: 19061

Table truncated, full table size 369 Kbytes.




Supplementary file Size Download File type/resource
GSM96135.tiff.tiff.gz 20.7 Mb (ftp)(http) TIFF

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