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Sample GSM462699 Query DataSets for GSM462699
Status Public on Mar 15, 2010
Title Malignant germ cell tumor_YST-9 [miRNA]
Sample type RNA
 
Channel 1
Source name Yolk sac tumor replicate 9
Organism Homo sapiens
Characteristics tumor composition: Pure
anatomical site: Ovary
gender: Female
age (yrs): 4
tumor stage: 4
Treatment protocol Nil; pre-treatment
Growth protocol Cell lines cultured under standard tissue culture conditions - incubated at 37C and in 5% CO2.
Extracted molecule total RNA
Extraction protocol TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Label Cy3
Label protocol Total RNA from each sample and the reference (the latter pooled First Choice Human RNA Survey Panel, Ambion, Austin, TX, USA) were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labeling kit (Exiqon, Vedbaek, Denmark). Microarrays were hybridized using a Tecan HS4800 hybridization station (Tecan, Grödig, Austria)
 
Channel 2
Source name First Choice Human RNA Survey Panel, Ambion, Austin, TX
Organism Homo sapiens
Characteristics reference: Pooled human RNA from 20 anatomical sites
Treatment protocol Nil; pre-treatment
Growth protocol Cell lines cultured under standard tissue culture conditions - incubated at 37C and in 5% CO2.
Extracted molecule total RNA
Extraction protocol TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Label Cy5
Label protocol Total RNA from each sample and the reference (the latter pooled First Choice Human RNA Survey Panel, Ambion, Austin, TX, USA) were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labeling kit (Exiqon, Vedbaek, Denmark). Microarrays were hybridized using a Tecan HS4800 hybridization station (Tecan, Grödig, Austria)
 
 
Hybridization protocol Test and reference RNA samples were mixed pair-wise and hybridized to the miRCURY LNA array platform version 9.2 (Exiqon, Vedbaek, Denmark), according to the manufacturer's instructions.
Scan protocol Arrays were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., Santa Clara, CA, USA), followed by image analysis using ImaGene 7.0 software (BioDiscovery, Inc., El Segundo, CA, USA).
Description Biological replicate 9 of 12
Data processing The resultant .txt files were processed using the Bioconductor package limma in the statistical software environment R. Within-array normalization was performed using the global loess method and between-array normalization using the Aquantile method.
VALUE = Post global loess normalization log2 ratios (test/reference)
 
Submission date Oct 18, 2009
Last update date Mar 11, 2010
Contact name Matthew Jonathan Murray
E-mail(s) mjm16@cam.ac.uk
Phone 07976413769
Organization name MRC Cancer Cell Unit
Department MRC/Hutchison Research Centre
Lab 2.5
Street address Box 197, Hills Road
City Cambridge
ZIP/Postal code CB2 0XZ
Country United Kingdom
 
Platform ID GPL9957
Series (1)
GSE18155 Malignant Germ Cell Tumors Display Common microRNA Profiles Resulting in Global Changes in Expression of mRNA Targets

Data table header descriptions
ID_REF
VALUE Post global loess normalization log2 ratios (test/reference)

Data table
ID_REF VALUE
-1 -0.362009781
0_Empty -0.116768783
10138 0.010000506
10170 -1.293773857
10234 0.203479545
10306 -2.277017193
10314 -2.689764322
10482 -2.382778575
10586 -1.005602606
10594 -2.434253739
10618 -2.834250738
10890 -4.093198319
10899 -0.380045069
1090 0.037270082
10901 0.155808682
10902 0.034966257
10903 -0.05216403
10904 -0.104812022
10905 -0.606833899
10906 -0.266608111

Total number of rows: 2242

Table truncated, full table size 40 Kbytes.




Supplementary file Size Download File type/resource
GSM462699_Cy3_Exiqon_13741564_S01_Cropped.txt.gz 922.2 Kb (ftp)(http) TXT
GSM462699_Cy5_Exiqon_13741564_S01_Cropped.txt.gz 903.2 Kb (ftp)(http) TXT
Processed data included within Sample table

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