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Sample GSM647486 Query DataSets for GSM647486
Status Public on Dec 31, 2010
Title HS 578T
Sample type RNA
 
Source name Cell line
Organism Homo sapiens
Characteristics barcode: 1_US45103081_13743024_S01_Cropped
sample tag: BR:HS578T
cell line: HS 578T
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 HS_578T_BR
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 12.56520307
17748 11.54098358
17888 7.551393641
17834 6.307900807
17749 11.04338185
19004 11.25810106
10914 11.28794478
17750 8.292219368
13169 6.518383711
17751 7.472519018
17813 6.285852914
17752 7.506501953
17829 6.463432269
19602 6.712962735
17845 6.523119991
9938 10.15293073
19580 9.95528045
17913 6.409517176
10916 6.568979078
30773 7.899953091

Total number of rows: 1151

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM647486.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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