|
| Status |
Public on Apr 29, 2020 |
| Title |
Expanding leaves_Day 3_Control, rep5 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
tissue: Expanding leaves (the next two leaves)
age: 13 days old (day 3 of Mg deprivation)
treatment: Control
|
| Treatment protocol |
Ten days after germination (day 0 of treatment), half of the plants were subjected to Mg deprivation (no Mg added).
|
| Growth protocol |
Arabidopsis thaliana ecotype Columbia-0 was grown hydroponically with the MGRL solution (Mg 1.5 mM) at 22ºC under a photoperiod of 16 h light (100 µmol m-2 s-1)/8 h darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mature leaves, expanding leaves and roots (ca. 10 mg) were collected, flash-frozen and lysed with lysis/binding buffer containing Sodium dodecyl sulphate. mRNA was isolated from the lysate by magnetic bead purification.
A strand-specific RNA-Seq library was constructed according to Townsley et al., Frontiers in Plant Science, 2015. Briefly, mRNA was fragmented and primed with 3' primer, cDNA was synthesised, and strand-specific 5’ adapter sequence was added and incorporated. The average fragment length of the constructed library was approximately 400 bp. All the libraries were pooled and subjected to 50 bp single-end sequencing with Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Ogura_Mg_12
Normalized_data_Expanding_leaves_Day3.csv
|
| Data processing |
Real Time Analysis (RTA) v1.18 performed base-calling.
Filtering, alignment and read count were performed on R software version 3.5.0 at the Linux operating system according to Ichihashi et al., Methods in Molecular Biology, 2018. Briefly, sequenced reads were trimmed for the first eight bases and low quality nucleotide at the end of reads, and short or low quality reads were removed. Filtered reads were mapped to the TAIR10 Arabidopsis reference genome sequence, and mapped reads were counted.
The count data were normalised on R software version 3.5.0 based on a trimmed mean of M- values (TMM) method. Normalization was performed for each set of control and Mg deficiency samples.
Genome_build: TAIR10 Arabidopsis reference genome
Supplementary_files_format_and_content: Tab-delimited CSV files contain normalized counts for each biological replicate.
|
| |
|
| Submission date |
Nov 07, 2019 |
| Last update date |
Apr 29, 2020 |
| Contact name |
Keitaro Tanoi |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Tokyo
|
| Department |
Graduate School of Agricultural and Life Sciences
|
| Street address |
1-1-1 Yayoi
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-0032 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE140070 |
Global transcriptomic analysis of Arabidopsis thaliana ecotype Columbia-0 subjected to magnesium deficiency |
|
| Relations |
| BioSample |
SAMN13230535 |
| SRA |
SRX7114832 |
