|
| Status |
Public on Nov 02, 2015 |
| Title |
UC remission Rectosigmoid area (R_R) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
rectosigmoid colon remission Ulcerative colitis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon Biopsy
phenotype: Remission UC patient
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using miRvana miRNa isolation kit following manufacturers instruction.
|
| Label |
Hy3
|
| Label protocol |
150 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
reference: Total RNA from Human Colon Biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon Biopsy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using miRvana miRNa isolation kit following manufacturers instruction.
|
| Label |
Hy5
|
| Label protocol |
150 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (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™ microRNA Array 7th gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction 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™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
|
| |
|
| Submission date |
Mar 16, 2015 |
| Last update date |
Nov 02, 2015 |
| Contact name |
Raju Ranjha |
| E-mail(s) |
raju_ranjha@yahoo.co.in
|
| Organization name |
Jawaharlala Nehru University
|
| Department |
School of Life Sciences
|
| Lab |
441
|
| Street address |
Lab. No.441, School of Life Sciences,
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
New Delhi-110067 |
| Country |
India |
| |
|
| Platform ID |
GPL19128 |
| Series (1) |
| GSE66932 |
Role of miRNA in inflammatory bowel disease |
|
