|
| Status |
Public on Dec 01, 2012 |
| Title |
Assay replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Dickeya dadantii infecting Acyrthosiphon pisum
|
| Organism |
Dickeya dadantii 3937 |
| Characteristics |
strain: 3937
growth protocol: grown inside aphid after inoculation by ingestion
|
| Treatment protocol |
For Control, bacterial cells were harvested by centrifugation before RNA extraction. For Assay, bacterial cells were separated from aphid cells fragments by centrifugation (10000g, 10 min, 4°C) on a discontinuous sucrose gradient (10% to 50%) before RNA extraction.
|
| Growth protocol |
For Control, Dickeya dadantii 3937 was grown 24h (O.D.600nm > 2) at 28°C in AP3 medium (Rahbé and Febvay, 1993. Entomol. Exp. Appl.. 67). For Assay, Dickeya dadantii was grown inside aphid Acyrthosiphon pisum after inoculation by ingestion (Grenier et al. 2006. Appl. Environ. Microbiol. 72)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol® reagent (Invitrogen) and the RNAprotect Bacterial reagent (Qiagen). DNA was removed by with DNase I of the TURBO DNAfree™ kit (Ambion). RNA quality was determined on agarose gel electrophoresis and concentration was determined at 260 nm using an ND 100 Nanodrop spectrophotometer (Thermo Fisher Scientific).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Nov 28, 2012 |
| Last update date |
Dec 01, 2012 |
| Contact name |
Yvan Rahbé |
| E-mail(s) |
[email protected]
|
| Phone |
+33 472437916
|
| URL |
http://keller-rahbe.eu
|
| Organization name |
INRA
|
| Department |
SPE
|
| Lab |
BF2I UMR203
|
| Street address |
INSA-Lyon, 20 ave. A.-Einstein
|
| City |
Villeurbanne |
| ZIP/Postal code |
69621 |
| Country |
France |
| |
|
| Platform ID |
GPL16335 |
| Series (1) |
| GSE42585 |
Expression analysis of Dickeya dadantii 3937 infecting an aphid (Acyrthosiphon pisum clone LL01) host |
|
