|
| Status |
Public on Aug 24, 2021 |
| Title |
KP_A_II_root |
| Sample type |
SRA |
| |
|
| Source name |
rice plants grown at three different positions in the growth chamber
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: root tip
cultivar: Kinandang Patong
|
| Growth protocol |
Two accessions were cultivated at three different positions in the growth chamber in the pot filled with the calcined clay (Profile® Greens GradeTM, PROFILE Products LLC, http://www.profileevs.com). The calcined clay was irrigated with a modified Kimura B culture solution (273.2 µM K2SO4, 546.9 µM MgSO4･7H2O, 182.0 µM NaH2PO4･2H2O, 182.3 µM CaCl2･2H2O, 182.4 µM CaSO4･2H2O, 1.2 mM KNO3, 411.2 µM NH4Cl, and 4 mg/L FeC6H5O7･nH2O [pH 5.5]) before sowing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted by the HighGI method (Yoshino et al., Breeding Science 2020).
Equal amounts of RNA extracted from three independent plants were pooled, then RNA-seq libraries were prepared using NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs) following manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were mapped to the IRGSP-1.0 genome assembly and MU7 gene models using the STAR aligner with options “--outFilterMultimapNmax 20 --outMultimapperOrder Random -- outSAMmultNmax 1 --alignIntronMax 3608 --twopassMode Basic”. Uniquely mapped read counts were quantified using the featureCounts (ver. 1.6.4) with options “-s 2 -p -B -C”.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for every genes for each sample.
|
| |
|
| Submission date |
Apr 06, 2021 |
| Last update date |
Aug 26, 2021 |
| Contact name |
Taiji Kawakatsu |
| E-mail(s) |
riverwin@affrc.go.jp
|
| Organization name |
National Agriculture and Food Research Organization
|
| Street address |
3-1-3 Kan-nondai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8604 |
| Country |
Japan |
| |
|
| Platform ID |
GPL23013 |
| Series (1) |
| GSE171578 |
iPOTs: Internet of Things-based pot system controlling optional treatment of soil water condition for plant phenotyping under drought stress |
|
| Relations |
| BioSample |
SAMN18636631 |
| SRA |
SRX10523059 |
