|
| Status |
Public on Mar 07, 2021 |
| Title |
WRC44_root |
| Sample type |
SRA |
| |
|
| Source name |
rice plants grown in the upland field
|
| Organism |
Oryza sativa |
| Characteristics |
accession: NARO WRC44
tissue: root tip
|
| Growth protocol |
Sixty one accessions were cultivated at an upland field of the Institute of Crop Science (National Agriculture and Food Research Organization, Ibaraki, Japan; 36°02′89″ N and 140°09′97″ E), on a volcanic ash soil of the Kanto loam type (Humic Andosol) in 2018. Fertilizer of 5.2 g N m–2, 15.4 g P2O5 m–2, and 5.6 g K2O m–2 was supplied before rice planting.
|
| 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 NovaSeq 6000 |
| |
|
| 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 |
Nov 30, 2020 |
| Last update date |
Mar 07, 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 |
GPL27660 |
| Series (2) |
| GSE162311 |
The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions [RNA-seq] |
| GSE162313 |
The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions |
|
| Relations |
| BioSample |
SAMN16954928 |
| SRA |
SRX9604451 |
