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Sample GSM5352144

Query DataSets for GSM5352144

Status

Public on Jun 02, 2021

Title

WFY1YE2

Sample type

SRA

Source name

leaf

Organism

Oryza sativa

Characteristics

variety type: WFYT025
Stage: on the first day after flowering
enviroment: early rice

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA).
Paired-end RNA-seq

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

WFY1YEVSWFY10YE_Gene_differential_expression

Data processing

A cDNA library constructed by technology from leaves of rice was sequenced run with Illumina 4000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence.
we aligned reads to rice reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.
Genome_build: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Osativa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

Submission date

Jun 01, 2021

Last update date

Jun 02, 2021

Contact name

Jianmin Bian

E-mail(s)

jmbian81@126.com

Organization name

江西农业大学

Street address

志敏大道1101