|
| Status |
Public on Sep 01, 2009 |
| Title |
Folsomia candida_desiccation_174hours_04 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Folsomia candida, desiccation, 174hours
|
| Organism |
Folsomia candida |
| Characteristics |
humidity: 98.2% Relative Humidity (desiccated groups)
time: 174hours
strain: 'Berlin' Strain; VU Amsterdam
test: ~25 pooled 25-27 day old individuals maintained at 98.2% Relative Humidity (desiccated groups)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Promega SV Total RNA isolation System
|
| Label |
Cy3
|
| Label protocol |
Agilent Low-Input Fluorescent Linear Amplification Kit was used to amplify and label 500 ng input material. The labelling reactions were performed in half of the volume recommended by Agilent. RNEasy (Qiagen) clean up was performed before hybridization.
|
| |
|
| Channel 2 |
| Source name |
Folsomia candida, reference, 174hours
|
| Organism |
Folsomia candida |
| Characteristics |
humidity: 100% Relative Humidity
time: 174hours
strain: 'Berlin' Strain; VU Amsterdam
reference: ~25 pooled 25-27 day old individuals maintained at 100% Relative Humidity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Promega SV Total RNA isolation System
|
| Label |
Cy5
|
| Label protocol |
Agilent Low-Input Fluorescent Linear Amplification Kit was used to amplify and label 500 ng input material. The labelling reactions were performed in half of the volume recommended by Agilent. RNEasy (Qiagen) clean up was performed before hybridization.
|
| |
|
| |
| Hybridization protocol |
Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization (4 rpm, 65 ºC, and 17 hours of incubation). Afterwards the array was washed using Agilent's Gene Expression Wash Buffer.
|
| Scan protocol |
An Agilent DNA microarray scanner in combination with Feature Extraction software (version 9.1.3.1) was used to measure fluorescence intensities.
|
| Description |
NA
|
| Data processing |
Data normalization was performed in R (http://www.R-project.org/) using the R/LIMMA (2.9.1) package (Smyth, 2005). Edward’s background correction (offset = 30) (Edwards, 2003) and global loess normalization (Yang et al., 2002) were applied.
|
| |
|
| Submission date |
May 15, 2009 |
| Last update date |
May 15, 2009 |
| Contact name |
Martijn Johannes Timmermans |
| Organization name |
Vrije Universiteit Amsterdam
|
| Department |
Animal Ecology
|
| Street address |
De Boelelaan 1085
|
| City |
Amsterdam |
| ZIP/Postal code |
1081HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6381 |
| Series (1) |
| GSE16127 |
Sugar sweet springtails: On the transcriptional response of Folsomia candida (Collembola) towards desiccation stress |
|
