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Sample GSM5227707 Query DataSets for GSM5227707
Status Public on Aug 24, 2021
Title KP_C_III_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 SAMN18636624
SRA SRX10523066

Supplementary file Size Download File type/resource
GSM5227707_TKTK060_3.tsv.gz 192.8 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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