|
| Status |
Public on Jun 25, 2015 |
| Title |
parafilm embedded tissue_normal adjacent_patient4 |
| Sample type |
RNA |
| |
|
| Source name |
parafilm embedded tissue_normal adjacent_patient4
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon Cancer Normal Adjacent
race: African American
data source: SBU
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each SBU FFPE sample, total RNA was isolated from three 10 µm thick tissue sections using a miRNeasy FFPE extraction kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. For each WU frozen samples, total RNA was extracted by Trizol followed by lithium precipitation (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol at the Siteman Cancer Center Tissue Procurement Facility. Total RNA quantity and quality was determined using a Nanodrop 2000C (Thermo Scientific, Waltham, MA).
|
| Label |
Cy3
|
| Label protocol |
The tissue RNAs (100 ηg) were labeled using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent Technologies)
|
| |
|
| Hybridization protocol |
The tissue RNAs (100 ηg) were labeled using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent Technologies) and used to probe and hybridized with Agilent Human Microarray Kit V3, 8 x 15K arrays, based on Sanger miRbase release 12.0 (G4470C, Agilent Technologies, Foster City, California).The hybridization was performed at 55o C for 20 h in an Agilent Hybridization Oven according to the manufacturer’s protocol.
|
| Scan protocol |
Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA)
|
| Data processing |
Features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.10.7.3.1) with default protocols and settings . The raw probe level data were imported into GeneSpring 12.5GX and the miRNA signal was normalized using the default setting: threshold raw signal to 1.0, percent shift to 90th percentile as the normalization algorithm and no baseline transformation.
|
| |
|
| Submission date |
Jun 25, 2013 |
| Last update date |
Jun 25, 2015 |
| Contact name |
Yuanhao Zhang |
| E-mail(s) |
yuanhao.zhang@stonybrook.edu
|
| Organization name |
Stony Brook University
|
| Department |
Applied Mathematics and Statistics
|
| Street address |
AMS Department,Stony Brook University
|
| City |
Stony Brook |
| ZIP/Postal code |
11790 |
| Country |
USA |
| |
|
| Platform ID |
GPL10850 |
| Series (1) |
| GSE48267 |
Differential Expression of miRNAs: Implication in Colon Cancer Racial Health Disparity |
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