|
| Status |
Public on Feb 19, 2018 |
| Title |
Col-0 mock_3dpi_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Col-0, mock treatment, 3dpi
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
background: Col-0
genotype: wild-type
age: 3-week-old
treatment: water (mock)
time: 3dpi
tissue: rosettes
|
| Treatment protocol |
3-week-old Arabidopsis plants were spray-inoculated with a spore suspension (4 x 10^6 spores/ml) of PcBMM (0.6 ml per pot containing 9 plants) or with water (mock treatment). After inoculation, plants were transferred to a growth chamber with a 10 h day/14 h night photoperiod, a temperature of 24ºC day/22ºC night, and light intensity was maintained at 120–150 umol m-2 s-1. Inoculated plants were kept under high humidity in covered trays. Samples were collected 1 and 3 days after inoculation and frozen in liquid nitrogen.
|
| Growth protocol |
Arabidopsis thaliana plants were grown in phytochambers on a sterilized mixture of soil and vermiculite (3:1) with a 10 h day/14 h night photoperiod, a temperature of 22ºC day/20ºC night and 50% relative humidity. Light intensity was fixed to 120–150 umol m-2 s-1 (Hernández-Blanco et al., 2007)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen samples were ground using mortar and pestle and total RNA was extracted with a phenol/chloroform method, as described in Berrocal-Lobo et al., 2002. Total RNA was further purified using the RNeasy Kit (Qiagen) and quantified with a NanoDrop ND-100 spectrophotometer (Thermo Scientific). RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies.
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized from 4 mg of total RNA using One-cycle target labeling and control reagents to produce biotin labeled cRNA.
|
| |
|
| Hybridization protocol |
The complementary RNA was used to hybridize ATH1 Arabidopsis GeneChip (Affymetrix) following the manufacturer’s protocol.
|
| Scan protocol |
The array images were analyzed with a GenePix 4000B scanner (Molecular Devices) at 10mm resolution.
|
| Description |
Gene expression at 3 days post-inoculation in mock-treated wild-type plants, replicate 2
Col_M3_2
Col-0, mock treatment, 3dpi, replicate 2
|
| Data processing |
The images were quantified with GenePix Pro 5.1.
|
| |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
Feb 19, 2018 |
| Contact name |
Sara Sopeña Torres |
| E-mail(s) |
[email protected]
|
| Organization name |
Centro de Biotecnologia y Genomica de Plantas (UPM-INIA)
|
| Street address |
Campus Montegancedo - Autovia M40 km.38
|
| City |
Madrid |
| ZIP/Postal code |
28223 |
| Country |
Spain |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE95609 |
Comparative transcriptional profiling of Arabidopsis yda11 mutant and wild-type plants after infection with Plectosphaerella cucumerina |
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