|
| Status |
Public on Dec 31, 2012 |
| Title |
C.elegans fed with CNCM I-3690 10 days rep2 |
| Sample type |
RNA |
| |
|
| Source name |
C.elegans fed with CNCM I-3690 for 10 days
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
diet: Lactobacillus rhamnosus CNCM I-3690
time: 10 days
|
| Growth protocol |
Synchronized populations were obtained from embryos isolated from gravid adults in the different feeding conditions. After feeding period (3 or 10 days) of worms were collected with M9 buffer, washed three times and collected in eppendorf tubes for worm disruption by sonication (3 pulses at 10 W, 20 s/pulse).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was performed with RNAasy Kit (Qiagen, Barcelona, Spain).
|
| Label |
biotin
|
| Label protocol |
Total RNA (300 ng per sample) was labeled using the Affymetrix GeneChip 3´GeneChip®3’ IVT Express Kit protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed as described by the manufacturer (Affymetrix, SantaClara, CA). The complementary RNA hybridization cocktail was incubated overnight at 45C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the Affymetrix-recommended protocol.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA)
|
| Description |
Gene expression data from C.elegans fed with CNCM I-3690 for 10 days
|
| Data processing |
Data analysis was accomplished in “R” (R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org) mainly through packages in the “Bioconductor” suite. Normalization was performed using rma (robust multi-array average expression measure) in “affy”.
|
| |
|
| Submission date |
Nov 09, 2012 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Tamara Fernandez-Calero |
| E-mail(s) |
[email protected]
|
| Phone |
00598 2 5220910
|
| Organization name |
Institut Pasteur de Montevideo
|
| Department |
Bioinfomatics Unit
|
| Street address |
Mataojo 2020
|
| City |
Montevideo |
| State/province |
Montevideo |
| ZIP/Postal code |
11400 |
| Country |
Uruguay |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE42192 |
Gene expression data from C.elegans |
|
