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Sample GSM462691 Query DataSets for GSM462691
Status Public on Mar 15, 2010
Title Malignant germ cell tumor_YST-1 [miRNA]
Sample type RNA
 
Channel 1
Source name Yolk sac tumor replicate 1
Organism Homo sapiens
Characteristics tumor composition: Mixed, within mature teratoma
anatomical site: Central nervous system
gender: Male
age (yrs): 12
tumor stage: 1
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 1 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 -0.113472125
0_Empty -0.031500243
10138 -0.978181073
10170 0.972023313
10234 0.241224784
10306 -1.189102941
10314 -4.380524667
10482 -0.332599025
10586 -0.078079461
10594 1.436176342
10618 -0.84507752
10890 -3.326595166
10899 0.175276193
1090 -0.082012687
10901 0.117206079
10902 0.171470883
10903 -0.037129147
10904 0.466137568
10905 0.235326955
10906 -0.044897841

Total number of rows: 2242

Table truncated, full table size 40 Kbytes.




Supplementary file Size Download File type/resource
GSM462691_Cy3_Exiqon_13741552_S01_Cropped.txt.gz 943.4 Kb (ftp)(http) TXT
GSM462691_Cy5_Exiqon_13741552_S01_Cropped.txt.gz 939.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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