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Sample GSM647512 Query DataSets for GSM647512
Status Public on Dec 31, 2010
Title HOP-92
Sample type RNA
 
Source name Cell line
Organism Homo sapiens
Characteristics barcode: 1_US45103081_13746343_S01_Cropped
sample tag: LC:HOP_92
cell line: HOP-92
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 HOP92_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 11.99071953
17748 11.26335588
17888 7.334868976
17834 6.325925458
17749 9.787362175
19004 10.50105284
10914 10.86881123
17750 7.390200884
13169 6.708914131
17751 7.827535316
17813 6.374479732
17752 7.245445135
17829 6.498714614
19602 6.516832735
17845 6.509741258
9938 8.121435135
19580 8.129862465
17913 6.346746246
10916 6.78166809
30773 7.660231315

Total number of rows: 1151

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM647512.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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