NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM541586 Query DataSets for GSM541586
Status Public on Jul 19, 2010
Title EPT294 ependynoma [human miRNA]
Sample type RNA
 
Source name patient sample
Organism Homo sapiens
Characteristics disease state: ependynoma primary tumor
age: 7
Sex: F
Treatment protocol tumors excised and flash frozen at distinct sites, storage and freezing method varies
Extracted molecule total RNA
Extraction protocol standard Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Cy3
Label protocol Cyanine-3 labeled miRNA was prepared from 100 ng total RNA using the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit, v.2.0 (June 2008) according to the manufacturer's instructions. No post labeling purification was performed, followed by vacuum drying of the labeled reactions, per the protocol.
 
Hybridization protocol Per the protocol, the dried labeled product was resuspended in nuclease-free water, followed by addition of Agilent GE Blocking Agent and Agilent Hi-RPM Hybridization Buffer. The labeled miRNA was then heated to 100°C for 5 minutes, followed by 5 minutes in an ice-water bath. The entire volume (45 µl) of eight, individual reactions was hybridized to Human 8x15K miRNA Microarrays (V2), Agilent #G4470B, for 20 hours at 55°C, 20 rpm, in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were immediately scanned after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 8x15k array slides, using the following scan settings: 20-bit, scan area 61x21.6 mm, single pass, scan resolution 5 µm, 100% PMT, green dye channel only, and eXtended Dynamic range (XDR) not enabled
Description analyzed at St. Jude Hartwell Center
Data processing The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters (protocol miRNA_105_Dec08 and Grid: 019118_D_20080215) to obtain background detrended processed signal intensities, which was then normalized, scaled and averaged. The minimum detecting miRNA expression signal was set at a threshold with less than 1% of the negative control probes.
 
Submission date May 05, 2010
Last update date Oct 08, 2010
Contact name Richard James Gilbertson
E-mail(s) richard.gilbertson@stjude.org
Organization name St Jude Children's Research Hospital
Department Developmental Neurobiology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL8227
Series (1)
GSE21687 Comparative genomics matches mutations and cells to generate faithful ependymoma models

Data table header descriptions
ID_REF
VALUE Normalized scaled signal intensity

Data table
ID_REF VALUE
ebv-miR-BART1-3p 12.88418
ebv-miR-BART1-5p .127746
ebv-miR-BART10 .1049323
ebv-miR-BART10* .1989009
ebv-miR-BART11-3p .1159243
ebv-miR-BART11-5p .1647505
ebv-miR-BART12 .1370763
ebv-miR-BART13 .099788
ebv-miR-BART13* .3028285
ebv-miR-BART14 .0247238
ebv-miR-BART14* .0693582
ebv-miR-BART15 .0542984
ebv-miR-BART16 .3077588
ebv-miR-BART17-3p .1521392
ebv-miR-BART17-5p .0130395
ebv-miR-BART18-3p .0225137
ebv-miR-BART18-5p .1093491
ebv-miR-BART19-3p 2.482685
ebv-miR-BART19-5p .0577724
ebv-miR-BART2-3p .0838836

Total number of rows: 799

Table truncated, full table size 17 Kbytes.




Supplementary file Size Download File type/resource
GSM541586.txt.gz 1.8 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap