|
| Status |
Public on Nov 01, 2008 |
| Title |
Hyperplasia tissue FFPE 2248 extraction 2 replica |
| Sample type |
RNA |
| |
|
| Source name |
lymphoid hyperplasia tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample age 1-2 years
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All samples contained at least 75% hyperplasia tissues without necrosis, which was confirmed by pathologist. The miRNAeasy kit (Qiagen, Mississauga, Canada) was used to extract total RNA (including miRNA) from frozen samples, The RecoverAll total RNA Isolation kit (Ambion, Streetsville, Canada) was used to extract total RNA (including miRNA) from FFPE samples
|
| Label |
Cy3 pCp
|
| Label protocol |
100ng total RNA was dephosphorylated at the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was then ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.0
|
| |
|
| Hybridization protocol |
labeled RNA was hybridized to Agilent miRNA array ( 8 arrays per slide) at 55°C for 22h in rotisserie in a hybridization oven. Disassembled arrays was washed in GE wash buffer 1&2 for 5 minutes each.
|
| Scan protocol |
Images was scanned with Agilent scanner at 5µm resolution
|
| Description |
slide 2
|
| Data processing |
The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed. See pdf file linked to Series for more information.
|
| |
|
| Submission date |
Aug 15, 2008 |
| Last update date |
Jan 29, 2010 |
| Contact name |
Harriet Feilotter |
| Organization name |
Queen's University
|
| Department |
Pathology and molecular department
|
| Lab |
microarray facility
|
| Street address |
88 Stuart St
|
| City |
Kingston |
| State/province |
Ontario |
| ZIP/Postal code |
K7L 3N6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL9081 |
| Series (1) |
| GSE12458 |
An array based analysis of miRNA expression comparing matched frozen and FFPE human tissue samples |
|
