|
| Status |
Public on Nov 14, 2013 |
| Title |
daf-16; daf-2 rsks-1-9 |
| Sample type |
RNA |
| |
|
| Source name |
C. elegans daf-16; daf-2 rsks-1
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genetic background: N2
genotype: daf-16; daf-2 rsks-1
phenotype: short-lived
|
| Growth protocol |
Synchronized C. elegans animals were growing at 15C until the late L4 stage and then transferred to 25C with FUDR (10ug / ml) for 48 hours before collection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using the Qiagen miRneasy Mini kit. The concentration and quality of total RNA samples were assessed using a Nanodrop and Agilent’s Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA was amplified for each experimental sample (Sigma TransPlex Complete Whole Transcriptome Amplification Kit). 1 μg of ds-cDNA was labeled with Cy3 for each experimental sample (NimbleGen One-Color DNA Labeling Kit). Total RNA extraction, amplification and labeling were randomized across experimental groups.
|
| |
|
| Hybridization protocol |
Sample hybridization was done according to the manufacturers’ protocol for the 12-plex Gene Expression array platform. 4 μg of each Cy3-labeled sample was loaded onto an array on the 12-plex chip. Hybridization was done overnight on a NimbleGen hybridization system 4 unit at 42°C for 16 hours.
|
| Scan protocol |
The 12-plex chip was washed, dried and scanned on a GenePix 4200A scanner at 300PMT, 100POW.
|
| Description |
This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the nineth of ten biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
Arrays were quantified using the NimbleScan2 software. RMA normalization using the limma package in R (Smyth, 2005 In Bioinformatics and Computational Biology Solutions using R and Bioconductor, V.J.C. Robert Gentleman, Wolfgang Huber, Rafael A. Irizarry and Sandrine Dudoit, ed. New York: Springer.) was used to normalize the expression data.
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| |
|
| Submission date |
Nov 13, 2013 |
| Last update date |
Nov 14, 2013 |
| Contact name |
Di Chen |
| Organization name |
Nanjing University
|
| Department |
Model Animal Research Center
|
| Street address |
12 Xuefu Rd, Pukou
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210061 |
| Country |
China |
| |
|
| Platform ID |
GPL17925 |
| Series (1) |
| GSE52340 |
Expression analysis of C. elegans wild-type N2 and rsks-1, daf-2, daf-2 rsks-1 and daf-16; daf-2 rsks-1 mutants |
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