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| Status |
Public on Aug 12, 2020 |
| Title |
Rice plants treated with D-Tagatose |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by array
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| Summary |
Rare sugars are monosaccharides that are rarely present in nature. To reveal a effect of D-tagatose in plant and the responses to the D-Tagatose in rice at gene expression level, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44K, custom-made; Agilent Technologies, Redwood City, CA, USA). As a result, there are no significant differences on the gene expression patterns between in mock- and D-tagatose-treated rice plants, and several PR-protein genes which had been reported to be induced by D-allulose or D-allose treatment, were compared by that with D-tagatose treatment in rice.
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| Overall design |
An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. By using RNeasy plant mini kit (Qiagen, Hilden, Germany), total RNA was extracted from shoots of two-leaf stage rice plants that had been treated with 0.5 mM D-tagatose or no sugar for 2 days. For each biological replicate, material from at least five rice plants was pooled to provide a single sample for RNA extraction. We performed 3 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (400 ng) was labeled with Cy-3 or Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2505B and software G2565BA; Agilent Technologies). Feature extraction software (version 9.1; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.
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| Contributor(s) |
Fukumoto T, Ohtani K, Mochizuki S, Ohara T, Akimitsu K |
| Citation(s) |
32759958 |
| Submission date |
Aug 26, 2019 |
| Last update date |
Aug 12, 2020 |
| Contact name |
Kazuya Akimitsu |
| E-mail(s) |
akimitsu.kazuya@kagawa-u.ac.jp
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| Phone |
+81-87-891-3131
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| Organization name |
Kagawa University
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| Department |
Faculty of Agriculture
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| Lab |
Plant pathology
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| Street address |
Ikenobe 2393
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| City |
Miki |
| State/province |
Kagawa |
| ZIP/Postal code |
761-0795 |
| Country |
Japan |
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| Platforms (1) |
| GPL6864 |
Agilent-015241 Rice Gene Expression 4x44K Microarray (Feature Number version) |
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| Samples (3) |
| GSM4044533 |
Mock vs D-Tagatose in shoot of rice replicate 1 |
| GSM4044534 |
Mock vs D-Tagatose in shoot of rice replicate 2 |
| GSM4044535 |
Mock vs D-Tagatose in shoot of rice replicate 3 |
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| Relations |
| BioProject |
PRJNA562163 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE136313_RAW.tar |
53.2 Mb |
(http)(custom) |
TAR (of TXT, XLS) |
| Processed data included within Sample table |
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