|
| Status |
Public on Apr 15, 2010 |
| Title |
Conjunctiva, sample 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
uninvolved conjunctiva tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: conjunctiva
patient: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was carried out using TRIzol® Reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kit (Qiagen, Valencia, CA) in accordance with the manufacturer’s procedure.
|
| Label |
Hy3
|
| Label protocol |
0.4 µg total RNA from sample and reference were 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 |
Common reference pool
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pterygium, conjunctiva
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was carried out using TRIzol® Reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kit (Qiagen, Valencia, CA) in accordance with the manufacturer’s procedure.
|
| Label |
Hy5
|
| Label protocol |
0.4 µg total RNA from sample and reference were 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 the 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).
|
| Description |
Half of each sample was taken and mixed to form the common reference pool. Each sample was then hybridized against this common reference, which can then be used as a common factor to which signals from all samples can be normalized, enabling direct comparison.
|
| Data processing |
A technical quality assessment was performed based on results from spike-in controls, flagging of spots, background intensity levels and signal intensity distribution. Image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized in Exiqon-R software using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
|
| |
|
| Submission date |
Apr 14, 2010 |
| Last update date |
Apr 14, 2010 |
| Contact name |
Silin Chen |
| E-mail(s) |
chen.silin@seri.com.sg
|
| Phone |
65 63275807
|
| Organization name |
Singapore Eye Research Institute
|
| Street address |
11 Third Hospital Avenue
|
| City |
Singapore |
| ZIP/Postal code |
168751 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL7723 |
| Series (1) |
| GSE21346 |
Differential regulation of microRNA in ocular wound healing |
|
