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Sample GSM93876 Query DataSets for GSM93876
Status Public on Feb 25, 2006
Title 5M CLL vs reference
Sample type RNA
 
Channel 1
Source name 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.
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 5M
Organism Homo sapiens
Characteristics B-CLL patient with mutated Ig genes
Extracted molecule total RNA
Label Cy5
 
 
Description 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 mg 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 of raw data
 
Submission date Jan 26, 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 -0.58 3071 808
2 0.00 12 13
3 -0.03 192 179
4 0.16 3730 5414
5 -0.01 1058 1033
7 -0.76 3075 531
8 -0.01 3562 3460
9 -0.02 2564 2422
11 0.03 363 391
13 0.06 365 417
14 -0.74 3146 566
15 0.02 6618 6924
16 0.03 950 1007
17 0.14 53 72
21 -0.84 3166 458
23 -0.08 175 145
25 0.07 104 123
26 -0.03 284 265
28 -0.99 3134 319
29 -0.02 1733 1644

Total number of rows: 19061

Table truncated, full table size 370 Kbytes.




Supplementary file Size Download File type/resource
GSM93876.tiff.tiff.gz 21.8 Mb (ftp)(http) TIFF

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