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Sample GSM522380 Query DataSets for GSM522380
Status Public on Mar 16, 2010
Title Adult_cortex_Hy5_Total RNA
Sample type RNA
 
Source name Adult_cortex_Total RNA
Organism Sus scrofa
Characteristics tissue: Adult_cortex
Extracted molecule total RNA
Extraction protocol The small and total RNA fractions were isolated from the individual tissues using the miRVana™ microRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) and TRI REAGENT® (Molecular Research Center, Inc., USA), respectively
Label Hy5
Label protocol A total of 200 ng and 1μg of the small RNA and total RNA fraction was used for each sample, respectively. 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 The miRCURY™ LNA microRNA Microarray version 9.2 was used for the array studies. Hybridization was performed in the hybridization station (Tecan Group Ltd., Männedorf, Switzerland), for 16 hours followed by stringent 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 Adult_cortex_Hy5_Total RNA
Data processing The text files, generated by Imagene v.7.0, were imported into the R environment (R Development Core Team (2007). The importing and pre-processing of data was performed using the Linear Models for Microarray Data (LIMMA) package [25]. The “normexp” background correction method [25] was applied. The intensities were then LOG 2 transformed and normalized, using the LIMMA implementation in quantile normalization. The intensities of four intra slide replicates were used to calculate average intensities of each hybridization signal. The data were filtered, firstly to include only human and porcine microRNA (hsa and ssc microRNAs, respectively) and secondly to exclude the probes which: a) showed little or no variation; b) their intensities in all cases were close to the background c) had more than 5 not available values; d) had range of linear intensities exceeding 100. The final, filtered data set consisted of intensity values for 240 probes (see supplementary data for complete list).
 
Submission date Mar 15, 2010
Last update date Mar 15, 2010
Contact name Agnieszka Podolska
E-mail(s) agap@life.ku.dk
Phone +4535333051
Organization name Faculty of Life Sciences, University of Copenhagen,
Department Department of Basic Animal and Veterinary Sciences
Street address Grønnegårdsvej 3 2nd floor
City Frederiksberg C
ZIP/Postal code 1870
Country Denmark
 
Platform ID GPL7724
Series (1)
GSE20893 MicroRNA expression profiling of the porcine developing brain

Data table header descriptions
ID_REF
VALUE log2 transformed intensities

Data table
ID_REF VALUE
17750 10.72925677
10971 9.114052886
10997 8.906540285
11026 9.934248096
11130 10.28583643
19580 13.01016854
10944 6.137683413
11030 13.71056246
10919 10.96969739
10978 8.293969605
10923 10.42764565
11039 12.51740784
11093 7.743938498
17327 7.485395624
17876 6.70273398
17510 9.252710741
11185 13.31245322
11181 7.283740406
17950 8.277595954
11184 10.23294311

Total number of rows: 231

Table truncated, full table size 4 Kbytes.




Supplementary file Size Download File type/resource
GSM522380.txt.gz 883.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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