|
| Status |
Public on Feb 09, 2012 |
| Title |
Slide 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
mutant 3/30
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: lin-28(n719); lin-46(ma164)
developmental stage: late L1 stage
|
| Growth protocol |
nematodes were grown on solid NGM media with E. coli as food source for 18 hours at 20°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the miRNA isolation kit (Ambion, Austin, TX, USA). The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
|
| Label |
Hy3
|
| Label protocol |
One µg total RNA from sample and reference 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 |
common reference pool
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
reference: common reference pool
|
| Growth protocol |
nematodes were grown on solid NGM media with E. coli as food source for 18 hours at 20°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the miRNA isolation kit (Ambion, Austin, TX, USA). The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
|
| Label |
Hy5
|
| Label protocol |
One µg total RNA from sample and reference 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 Other Species (Exiqon, Denmark), which contains capture probes targeting all miRNAs for other species than human, mouse or rat registered in the miRBASE version 14.0 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 |
mutant biological replicate 3
|
| 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.
|
| |
|
| Submission date |
Feb 08, 2012 |
| Last update date |
Feb 10, 2012 |
| Contact name |
Eric Moss |
| E-mail(s) |
mosseg@umdnj.edu
|
| Phone |
8565662896
|
| Fax |
8565662691
|
| Organization name |
UMDNJ
|
| Department |
Molecular Biology
|
| Street address |
2 Medical Center Dr.
|
| City |
Stratford |
| State/province |
NJ |
| ZIP/Postal code |
08084 |
| Country |
USA |
| |
|
| Platform ID |
GPL15202 |
| Series (1) |
| GSE35634 |
Effect of lin-28 and lin-46 on miRNA profile in late L1 stage Caenorhabditis elegans |
|
