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Sample GSM593269 Query DataSets for GSM593269
Status Public on Sep 14, 2010
Title F50 cortex_rep2
Sample type RNA
 
Source name F50 cortex, small RNA fraction
Organism Sus scrofa
Characteristics breed: crossbreed between Landrace, Yorkshire and Duroc
tissue: cortex
developmental stage: gestation day 50
Extracted molecule total RNA
Extraction protocol The small RNA fractions were isolated from the individual tissues using the miRVana™ microRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA).
Label Hy3
Label protocol A total of 200 ng of small RNA fraction 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 The miRCURY™ LNA microRNA Microarray version 11.0 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 Slides were dried and scanned. The analysis was 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 F50_cortex_small RNA fraction
Data processing The text files, generated by Imagene v.8.0, were imported into Rosetta Resolver and normalized as previously described:
Book: MicroRNA Profiling in Cancer: A Bioinformatics perspective. 2009. Editor Yuriy Gusev. Chapter: Søkilde R, Kaczkowski B, Barken K B, Mouritzen P, Møller S, Litman T. "MicroRNA Expression Analysis by LNA Enhanced Microarrays".
Data was filtered by using probes showing a standard deviation (SD) above 0.1. The final, filtered data set consisted of intensity values for 1088 probes. All clustering and statistical analysis was performed in TMeV. PCA plot of samples was performed using all 1088 probes, by using a median centering of the data set. For the two-way hierarchical clustering, the 181 probes on the array annotated as pig microRNAs was used (see the 'GSE24106_pig_annotation.txt' supplementary file). In case of lack of annotation in pig, human probes were used. The 1- Pearson correlation coefficient was used as a distance metric. Each probe is mean-centered and compared to the mean expression.
 
Submission date Sep 13, 2010
Last update date Sep 14, 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 GPL7723
Series (1)
GSE24106 MicroRNA expression profiling of the porcine developing cortex and cerebellum

Data table header descriptions
ID_REF
VALUE Normalized log2 signal

Data table
ID_REF VALUE
11279 11.81246
11278 10.25225
46207 9.73742
11184 10.25187
42708 11.14455
11182 10.36927
11181 7.95827
42527 6.4933
17718 9.23998
42728 9.02068
4040 15.30431
46259 7.61867
42633 6.32999
28759 7.6324
28703 7.34598
27568 9.36159
29190 10.23239
29490 11.08536
17870 7.96224
28966 7.38156

Total number of rows: 1088

Table truncated, full table size 14 Kbytes.




Supplementary file Size Download File type/resource
GSM593269.txt.gz 920.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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