NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM638906 Query DataSets for GSM638906
Status Public on Apr 12, 2011
Title striatum_D2.6 MouseRef-8
Sample type RNA
 
Source name striatum, adult, naïve
Organism Mus musculus
Characteristics gender: male
strain: DBA/2J
developmental stage: adult
tissue: brain striatum
Extracted molecule total RNA
Extraction protocol TRIzol total RNA extraction
Label biotinylated UTP nucleotide
Label protocol Total RNA that has passed the QC tests will be amplified using the TotalPrep RNA Amplification Kit (Ambion), which can amplify RNA across a range from 50 to 500 ng. The resultant amplified RNA (aRNA) incorporates a biotinylated UTP nucleotide.
 
Hybridization protocol An aliquot of aRNA is hybridized to an Illumina BeadChip using proprietary buffers, first at 65⁰C for thirty minutes, then overnight at 58⁰C.
Scan protocol The arrays are washed and then stained with Cy3-streptavidin, washed again, and then scanned on an Illumina BeadStation bead array scanner.
Data processing Data from the scanner is consolated using the GenomeStudio software. Built in quality control measures are monitored in GenomeStudio to look for obvious problems in the hybridization process. Final output is customized to allow use of a variety of statistical packages, including BioConductor and GeneSifter.
 
Submission date Dec 13, 2010
Last update date Apr 12, 2011
Contact name Nicole Walter
E-mail(s) waltern@ohsu.edu
Organization name Oregon Health & Science University
Department Behavioral Neuroscience
Lab Grant Lab
Street address 3181 SW Sam Jackson Park Road
City Portland
State/province OR
ZIP/Postal code 97239
Country USA
 
Platform ID GPL6885
Series (1)
GSE26024 Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarray

Data table header descriptions
ID_REF
VALUE The data was transformed using lumi with the variance stabilization transformation (VST) and normalized using the robust spline normalization (RSN). The threshold for a probe to detect expression as ‘present’ was set at p < 0.05 as determined by lumi. Only present probes are reported in the normalized data.

Data table
ID_REF VALUE
ILMN_2971845 9.982231448
ILMN_1214700 8.972199832
ILMN_3071356 8.888030256
ILMN_2516348 13.49516065
ILMN_2517170 9.575852819
ILMN_3114339 9.003183092
ILMN_1229042 11.67010087
ILMN_2632942 11.40210741
ILMN_2776910 8.996369777
ILMN_2591592 9.249488432
ILMN_3058640 8.996078932
ILMN_3152328 14.13426377
ILMN_2895546 9.145408517
ILMN_1237404 9.041374605
ILMN_2693258 9.981584359
ILMN_1221275 9.07068719
ILMN_3148398 8.919991413
ILMN_3079421 10.8383943
ILMN_2639036 9.85133971
ILMN_2960308 10.94347509

Total number of rows: 14185

Table truncated, full table size 344 Kbytes.




Supplementary data files not provided
Processed data are available on Series record
Processed data included within Sample table

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