|
| Status |
Public on Mar 15, 2010 |
| Title |
Benign germ cell tumor_MT-34 [miRNA] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mature teratoma replicate 3
|
| Organism |
Homo sapiens |
| Characteristics |
tumor composition: Mixed, within yolk sac tumor
anatomical site: Ovary
gender: Female
age (yrs): 12
tumor stage: Mature
|
| 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 6 of 6
|
| 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 |
|
