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Sample GSM4996741 Query DataSets for GSM4996741
Status Public on Jan 01, 2021
Title D8627d1
Sample type SRA
 
Source name seed
Organism Helianthus annuus
Characteristics tissue: seed
cultivar: cultivars "86-1"
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
City Harbin
ZIP/Postal code 150030
Country China
 
Platform ID GPL29551
Series (1)
GSE164103 Comparative transcriptomic analyses of high and low oleic acid content sunflower (Helianthus annuus L.) seed development
Relations
BioSample SAMN17191186
SRA SRX9764193

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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