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Sample GSM96136 Query DataSets for GSM96136
Status Public on Feb 25, 2006
Title 42NM 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 42NM
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 -0.66 5119 1117
2 -0.20 77 48
3 -0.23 322 191
4 0.00 4934 4909
5 -0.13 1119 837
7 -1.20 4384 274
8 -0.03 3433 3192
9 -0.07 2223 1894
11 -0.06 314 272
13 0.03 370 398
14 -1.22 4163 248
15 0.02 5501 5756
16 0.09 609 756
17 0.16 39 56
21 -1.26 4306 236
23 -0.07 228 196
25 -0.13 203 149
26 -0.04 218 199
28 -1.24 4252 245
29 0.06 2025 2327

Total number of rows: 19061

Table truncated, full table size 367 Kbytes.




Supplementary file Size Download File type/resource
GSM96136.tiff.tiff.gz 20.5 Mb (ftp)(http) TIFF

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