|
| Status |
Public on Nov 22, 2010 |
| Title |
LENS, replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from lenses of adult mice (LENS 2)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lens
strain: C57BL/6J
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with the miRNeasy kit (Qiagen)
|
| Label |
Hy3
|
| Label protocol |
One µg total RNA from sample and reference (Eye sample) was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
Total RNA from entire eyeballs from adult mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Entire Eyeball
strain: C57BL/6J
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with the miRNeasy kit (Qiagen)
|
| Label |
Hy5
|
| Label protocol |
One µg total RNA from sample and reference (Eye sample) was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| |
| Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 12.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
|
| Scan protocol |
After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).
|
| Description |
(4) (LENS 2)
Slide 4
present call rate per slide: 0.644891122278057
Hy3 raw: 1_Exiqon_13973493_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973493_S01_Cropped.txt
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Project_Summary Report version 3.5 results presented in Sample data tables.
When calling of a particular miRNA failed on an array this is indicated by the acronym null. The criteria for deciding that the calling of a miRNA had failed on a particular array, was that 3 or more of the 4 replicated measures of this miRNA were flagged (i.e. the signal is below background) by the image analysis software. Further, all capture probes with Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide is indicated by the acronym null.
|
| |
|
| Submission date |
Oct 05, 2010 |
| Last update date |
Nov 17, 2010 |
| Contact name |
Marianthi Karali |
| E-mail(s) |
karali@tigem.it
|
| Organization name |
Telethon Institute for Genetics & Medicine (TIGEM)
|
| Street address |
Via Pietro Castellino, 111
|
| City |
Naples |
| ZIP/Postal code |
80131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL7723 |
| Series (1) |
| GSE22882 |
microRNA profiling in Mouse Eye: Retina, Lens, Cornea, Retinal Pigment Epithelium |
|
