|
| Status |
Public on Apr 29, 2009 |
| Title |
Barley root gene expression 7d Treatment: Mock, Replication II |
| Sample type |
RNA |
| |
|
| Source name |
root tissue
|
| Organism |
Hordeum vulgare |
| Characteristics |
Roots of seedlings 7 day after P.indica-treatment. Treatment was performed 2 days after germination. Dissected root tissue from 40 plants was pooled. Samples were harvested in the afternoon.
|
| Biomaterial provider |
Institute of Phytopathology and Applied Zoology, Justus-Liebig-Universität Gießen
|
| Treatment protocol |
P. indica was grown on solid complete media, scratched from the media with a spatula and resuspended in water to 500.000 spores per ml. Seedlings were dip-inoculated for two hours and thereafter transferred to a seramis/oil dri mixture (v.v 2:1) (described in Proc Natl Acad Sci USA 103: 18450-18457)
|
| Growth protocol |
Barley plants of the cultivar Golden Promise were germinated for two days in the dark at RT. After inoculation, plants were grown in a phytochamber in a 16 h / 8 h light-dark cycle. Temperature was 22°C and 18°C, relative humidity 60% during light and dark periods, respectively. Five seedlings were planted per pot in a mixture of Seramis/oil dri (v.v 2:1).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation, material from 40 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer’s instructions, respectively.
|
| Label |
Cy3
|
| Label protocol |
Cy3-labeled cRNA were prepared according to the standard Agilent protocol from 500 ng total RNA (One-Color Microarray-based Gene Expression analysis, version 5.0.1).
|
| |
|
| Hybridization protocol |
Following fragmentation, 1,65 ug of cRNA were hybridized for 17 hr at 65°C on 4 x 44K Barley Agilent Array. Arrays were washed accroding to the protocol (One-Color Microarray-based Gene Expression analysis, version 5.0.1).
|
| Scan protocol |
Microarrays were scanned on an Agilent Microarray Scanner.
|
| Description |
HV_7d_Mock_II
|
| Data processing |
Raw data were generated with the Agilent Microarray Scanner and the feature extraction software FE Version 9.5.3.1 (Agilent, Waldbronn, Germany), The raw data contains 2,600 replicate probes and internal controls. Data analysis was performed by Biconductor/R (http://www.bioconductor.org/). Raw data were read by read.maimage function of R, filtered in order to remove replicate probes and internal controls. Background corrected intensities (gProcessedSignal) lower then 1 were set to 1 (in order to avoid negative values), converted by log2 and normalised by the quantile normalisation (normalizeQuantiles).
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| |
|
| Submission date |
Nov 27, 2008 |
| Last update date |
Apr 29, 2009 |
| Contact name |
Patrick Schaefer |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Phytopathology and Applied Zoology
|
| Street address |
Heinrich-Buff-Ring 26-32
|
| City |
Giessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL7659 |
| Series (1) |
| GSE13756 |
Barley root gene expression during colonisation by Piriformospora indica |
|
