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Sample GSM647465 Query DataSets for GSM647465
Status Public on Dec 31, 2010
Title IGROV1
Sample type RNA
 
Source name Cell line
Organism Homo sapiens
Characteristics barcode: 1_US45103081_13733310_S01_Cropped
sample tag: OV:IGROV1
cell line: IGROV1
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the individual cell lines using Trizol (Invitrogen)
Label Hy3
Label protocol A total of 1000 ng of total RNA was used for each sample. MiRCURY™ LNA microRNA Power labeling Kit (Exiqon, Vedbaek, Denmark) was used following the manufacturers’ recommendations. Spike-ins (used as control probes) were added in equal amounts to each reaction and labeled.
 
Hybridization protocol Hybridization was performed in the hybridization station (Tecan Group Ltd., Männedorf, Switzerland), for 16 hours followed by stringency washes.
Scan protocol Subsequently, slides were dried and scanned. The analysis were performed using the relevant GenePix® Array Lists (GAL files) www.exiqon.com.
The arrays were scanned by the Agilent scanner (Agilent Technologies, Santa Clara, CA, USA), to generate Tagged Image File Format (TIFF) images. The intensities were converted to digital values using Imagene version 7.0 software. The quality control of the spots was performed by the software and adjusted manually.
Description IGR_OV1_OV
Data processing The text files, generated by Imagene v.8.0, were imported into Rosetta Resolver and normalized as previously described. The data used are median of replicate spots from normalized values using the Quantile normalization method in limma package in R version 11 as descriped in Søkilde et al. (MICRORNA EXPRESSION ANALYSIS BY LNA ENHANCED MICROARRAYS)
 
Submission date Dec 30, 2010
Last update date Dec 31, 2010
Contact name Rolf Søkilde
E-mail(s) rolf.soekilde@gmail.com
Organization name Lund University, Sweden
Department Department of Oncology
Street address Scheelevägen 2
City Lund
ZIP/Postal code 221 85
Country Sweden
 
Platform ID GPL11039
Series (1)
GSE26375 MicroRNA expression profiling using microRNA microarrays on NCI-60 cell lines.

Data table header descriptions
ID_REF
VALUE normalized log2 Expression

Data table
ID_REF VALUE
3320 11.40137087
17748 10.55973898
17888 6.814928063
17834 6.398006998
17749 9.31100761
19004 9.755921714
10914 10.29586603
17750 7.368351042
13169 6.521717878
17751 6.925301281
17813 6.214538444
17752 6.853993615
17829 6.363388824
19602 6.588025829
17845 6.412911859
9938 8.487395948
19580 8.407376575
17913 6.226051848
10916 6.483495876
30773 7.576642877

Total number of rows: 1151

Table truncated, full table size 19 Kbytes.




Supplementary file Size Download File type/resource
GSM647465.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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