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Sample GSM4996748

Query DataSets for GSM4996748

Status

Public on Jan 01, 2021

Title

L27d2

Sample type

SRA

Source name

seed

Organism

Helianthus annuus

Characteristics

tissue: seed
cultivar: cultivars "L-1-OL-1"
developmental stage: 27d after flowering

Treatment protocol

The two cultivars (86-1, L-1-OL-1) in two different seed developmental stages (oleic acid accumulated rapidly at 17 DAF, and kept relatively stable at 27 DAF) for transcriptome sequencing

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using RNAprep pure Plant Kit
RNA libraries were prepared for sequencing using Illumina novaseq 6000 platform

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Illumina novaseq 6000 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Helianthus+annuus
Supplementary_files_format_and_content: Excels include FPKM values for each Sample

Submission date

Dec 31, 2020

Last update date

Jan 02, 2021

Contact name

Jian Wang

E-mail(s)

wangjian8@genomics.cn

Organization name

Northeast Agricultural University

Street address

600 Changjiang Road