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| Status |
Public on Apr 29, 2020 |
| Title |
Global transcriptomic analysis of Arabidopsis thaliana ecotype Columbia-0 subjected to magnesium deficiency |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Magnesium (Mg) is essential for many biological processes in plant cells and its deficiency causes yield reduction in crop systems. Low Mg status reportedly impacts on photosynthesis, sucrose partitioning and biomass allocation. However, earlier responses to Mg deficiency are scarcely described. Generally, symptoms of nutrient deficiency appear in specific ages of leaves. Therefore, we hypothesised that transcriptional responses to Mg deficiency are different depending on the ages of leaves, and performed a global transcriptomic analysis in two types of leaves; source and sink leaves of the model plant species Arabidopsis thaliana to reveal the earlier responses to Mg deficiency. The global transcriptomic study revealed that short-term Mg deficiency triggers the expression of defence response genes in sink leaves. In roots, although short-term Mg deficiency enhanced the Mg2+ uptake from the environmnet, transcriptional levels of genes encoding putative Mg2+ transporters in roots were unchanged, suggesting non-transcriptional regulation of Mg2+ uptake in roots.
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| Overall design |
mRNA was extracted from mature (source) and expanding (sink) leaves of control and Mg-deficient Arabidopsis at days 3, 5 and 8 of Mg deprivation treatment and roots at day 3. Three to six biological replicates were selected based on the quality of RNA.
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| Web link |
https://www.frontiersin.org/articles/10.3389/fpls.2020.00563/abstract
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| Contributor(s) |
Ogura T, Kobayashi NI, Ichihashi Y, Shibata A, Shirasu K, Nakanishi TM, Tanoi K |
| Citation(s) |
32582226 |
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| Submission date |
Nov 07, 2019 |
| Last update date |
Jun 29, 2020 |
| Contact name |
Keitaro Tanoi |
| E-mail(s) |
[email protected]
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| Organization name |
The University of Tokyo
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| Department |
Graduate School of Agricultural and Life Sciences
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| Street address |
1-1-1 Yayoi
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| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-0032 |
| Country |
Japan |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (58)
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| GSM4153618 |
Mature leaves_Day 3_Control, rep4 |
| GSM4153619 |
Mature leaves_Day 3_-Mg, rep1 |
| GSM4153620 |
Mature leaves_Day 3_-Mg, rep2 |
| GSM4153621 |
Mature leaves_Day 3_-Mg, rep3 |
| GSM4153622 |
Mature leaves_Day 5_Control, rep1 |
| GSM4153623 |
Mature leaves_Day 5_Control, rep2 |
| GSM4153624 |
Mature leaves_Day 5_Control, rep3 |
| GSM4153625 |
Mature leaves_Day 5_Control, rep4 |
| GSM4153626 |
Mature leaves_Day 5_Control, rep5 |
| GSM4153627 |
Mature leaves_Day 5_-Mg, rep1 |
| GSM4153628 |
Mature leaves_Day 5_-Mg, rep2 |
| GSM4153629 |
Mature leaves_Day 5_-Mg, rep3 |
| GSM4153630 |
Mature leaves_Day 8_Control, rep1 |
| GSM4153631 |
Mature leaves_Day 8_Control, rep2 |
| GSM4153632 |
Mature leaves_Day 8_Control, rep3 |
| GSM4153633 |
Mature leaves_Day 8_Control, rep4 |
| GSM4153634 |
Mature leaves_Day 8_-Mg, rep1 |
| GSM4153635 |
Mature leaves_Day 8_-Mg, rep2 |
| GSM4153636 |
Mature leaves_Day 8_-Mg, rep3 |
| GSM4153637 |
Mature leaves_Day 8_-Mg, rep4 |
| GSM4153638 |
Expanding leaves_Day 3_Control, rep1 |
| GSM4153639 |
Expanding leaves_Day 3_Control, rep2 |
| GSM4153640 |
Expanding leaves_Day 3_Control, rep3 |
| GSM4153641 |
Expanding leaves_Day 3_Control, rep4 |
| GSM4153642 |
Expanding leaves_Day 3_Control, rep5 |
| GSM4153643 |
Expanding leaves_Day 3_-Mg, rep1 |
| GSM4153644 |
Expanding leaves_Day 3_-Mg, rep2 |
| GSM4153645 |
Expanding leaves_Day 3_-Mg, rep3 |
| GSM4153646 |
Expanding leaves_Day 3_-Mg, rep4 |
| GSM4153647 |
Expanding leaves_Day 5_Control, rep1 |
| GSM4153648 |
Expanding leaves_Day 5_Control, rep2 |
| GSM4153649 |
Expanding leaves_Day 5_Control, rep3 |
| GSM4153650 |
Expanding leaves_Day 5_Control, rep4 |
| GSM4153651 |
Expanding leaves_Day 5_Control, rep5 |
| GSM4153652 |
Expanding leaves_Day 5_-Mg, rep1 |
| GSM4153653 |
Expanding leaves_Day 5_-Mg, rep2 |
| GSM4153654 |
Expanding leaves_Day 5_-Mg, rep3 |
| GSM4153655 |
Expanding leaves_Day 8_Control, rep1 |
| GSM4153656 |
Expanding leaves_Day 8_Control, rep2 |
| GSM4153657 |
Expanding leaves_Day 8_Control, rep3 |
| GSM4153658 |
Expanding leaves_Day 8_Control, rep4 |
| GSM4153659 |
Expanding leaves_Day 8_-Mg, rep1 |
| GSM4153660 |
Expanding leaves_Day 8_-Mg, rep2 |
| GSM4153661 |
Expanding leaves_Day 8_-Mg, rep3 |
| GSM4153662 |
Expanding leaves_Day 8_-Mg, rep4 |
| GSM4153663 |
Expanding leaves_Day 8_-Mg, rep5 |
| GSM4153664 |
Root_Day 3_Control, rep1 |
| GSM4153665 |
Root_Day 3_Control, rep2 |
| GSM4153666 |
Root_Day 3_Control, rep3 |
| GSM4153667 |
Root_Day 3_Control, rep4 |
| GSM4153668 |
Root_Day 3_Control, rep5 |
| GSM4153669 |
Root_Day 3_Control, rep6 |
| GSM4153670 |
Root_Day 3_-Mg, rep1 |
| GSM4153671 |
Root_Day 3_-Mg, rep2 |
| GSM4153672 |
Root_Day 3_-Mg, rep3 |
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| Relations |
| BioProject |
PRJNA588176 |
| SRA |
SRP229078 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140070_Normalized_data_Expanding_leaves_Day3.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE140070_Normalized_data_Expanding_leaves_Day5.csv.gz |
1.2 Mb |
(ftp)(http) |
CSV |
| GSE140070_Normalized_data_Expanding_leaves_Day8.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE140070_Normalized_data_Mature_leaves_Day3.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE140070_Normalized_data_Mature_leaves_Day5.csv.gz |
1.2 Mb |
(ftp)(http) |
CSV |
| GSE140070_Normalized_data_Mature_leaves_Day8.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE140070_Normalized_data_Root_Day3.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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