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Sample GSM647494 Query DataSets for GSM647494
Status Public on Dec 31, 2010
Title EKVX
Sample type RNA
 
Source name Cell line
Organism Homo sapiens
Characteristics barcode: 1_US45103081_13743306_S01_Cropped
sample tag: LC:EKVX
cell line: EKVX
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 EKVX_LUN
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 11.8410232
17748 11.00487557
17888 7.026884793
17834 6.395543767
17749 10.07372478
19004 10.42992379
10914 11.06098718
17750 8.286470685
13169 6.598239607
17751 7.967122572
17813 6.265933538
17752 7.057690222
17829 6.498076052
19602 6.563733512
17845 6.590425616
9938 8.635877409
19580 8.525346112
17913 6.325460203
10916 6.580067746
30773 8.046047661

Total number of rows: 1151

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM647494.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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