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Sample GSM6234250

Query DataSets for GSM6234250

Status

Public on Jun 10, 2022

Title

mock, 150mM, root, sample 3

Sample type

SRA

Source name

root

Organism

Oryza sativa

Characteristics

tissue: root
genotype: wild type
treatment: mock
treatment: 150mM NaCl
time: 8 weeks post inoculation

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from 100 mg shoot or root tissue by using TRIzol Reagent (Invitrogen™) following the manufacturer’s instructions. A total amount of RNA (≥ 4 μg) per sample were used for transcriptome sequencing.
Strand-specific sequencing libraries were obtained following the handbook for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

The quality control of raw reads was evaluated using FastQC software v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The low-quality reads (Q-value < 20) and adaptors were removed using the sequence preprocessing tool Trimmomatic v0.39 (Bolger et al., 2014). After low-quality reads and adaptors were removed, all cleaned reads were assembled into contigs using Trinity (Grabherr et al., 2011).
To get a more specific gene list, we used CD-HIT-EST version CD-HIT4 to cluster the redundancy of transcripts and removed the shorter redundant transcripts (Li and Godzik, 2006;Fu et al., 2012).
In this analysis, Bowtie2 version V2.3.2 and RSEM version v1.2.31 software were used to map short reads to the Trinity de novo assembly and quantify the read counts that matched to each contig (Li and Dewey, 2011;Langmead and Salzberg, 2012). Then, Transdecoder was used to identify candidate coding regions for gene prediction.
Next, to distinguish the de novo assembled sequences between those of the rice and fungal species, the Basic Local Alignment Search Tool (BLAST) searches against the Orygenes database (https://orygenesdb.cirad.fr/) for rice (O. sativa) and the National Center for Biotechnology Information (NCBI) database for AM fungi (R. irregularis), was performed for annotation, respectively (Altschul et al., 1990;Droc et al., 2006;Coordinators, 2016).
Assembly: Orygenes database (https://orygenesdb.cirad.fr/) for rice (O. sativa) and the National Center for Biotechnology Information (NCBI) database for AM fungi (R. irregularis)
Supplementary files format and content: tab-delimited excel files include raw count values for each Sample

Submission date

Jun 10, 2022

Last update date

Jun 10, 2022

Contact name

Shu-Yi Yang

E-mail(s)

shuyiyang@ntu.edu.tw

Phone

+886-2-3366-2533

Organization name

Institute of Plant Biology