|
| Status |
Public on Nov 23, 2020 |
| Title |
IMA2OX-2 +Fe Root |
| Sample type |
SRA |
| |
|
| Source name |
iron-sufficient roots
|
| Organism |
Oryza sativa |
| Characteristics |
iron status: iron-sufficient
cultivar: Tsukinohikari
tissue: roots
genotype: OsIMA2 overexpression line 2
|
| Treatment protocol |
Iron-sufficiency treatment (which is same as preculture condition) or iron-deficiency treatment for 7 days was imposed after preculture in hydroponics
|
| Growth protocol |
Rice (Oryza sativa L.) cultivar Tsukinohikari and its transformants were germinated and cultured hydroponically based on the description in Kobayashi et al. (2019) Plant Mol. Biol. 101:471-486.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from hydroponically grown roots and leaves using the RNeasy Plant Mini Kit (QIAGEN), treated with DNase I and reverse-transcribed using ReverTra Ace qRT-PCR RT Master Mix with gDNA Remover (TOYOBO).
RNA libraries were prepared for sequencing using Lasy-Seq v1.1 (Kamitani et al., (2019) Scientific Reports)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 6
|
| Data processing |
Preprocessing was performed using trimmomatic version 0.39
Mapping was performed using bowtie version 1.2.3
Quantification of expression was performed using RSEM version 1.2.21
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Text files including RPM values for each sample.
|
| |
|
| Submission date |
Jun 06, 2020 |
| Last update date |
Nov 23, 2020 |
| Contact name |
Takanori Kobayashi |
| E-mail(s) |
[email protected]
|
| Phone |
+81 76 227 7505
|
| Organization name |
Ishikawa Prefectural University
|
| Department |
Research Institute for Bioresources and Biotechnology
|
| Street address |
1-308 Suematsu
|
| City |
Nonoichi |
| State/province |
Ishikawa |
| ZIP/Postal code |
921-8836 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19290 |
| Series (2) |
| GSE151939 |
Round 2 RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice. |
| GSE151941 |
RNA-sequencing analysis of the OsIMA overexpression and knockdown rice lines and Fe deficiency responsiveness of non-transformant (NT) rice |
|
| Relations |
| BioSample |
SAMN15154497 |
| SRA |
SRX8485265 |
