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Status |
Public on Jan 01, 2021 |
Title |
D8627d1 |
Sample type |
SRA |
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Source name |
seed
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Organism |
Helianthus annuus |
Characteristics |
tissue: seed cultivar: cultivars "86-1" developmental stage: 27d after flowering
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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
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Dec 31, 2020 |
Last update date |
Jan 02, 2021 |
Contact name |
Jian Wang |
E-mail(s) |
wangjian8@genomics.cn
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Organization name |
Northeast Agricultural University
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Street address |
600 Changjiang Road
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City |
Harbin |
ZIP/Postal code |
150030 |
Country |
China |
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Platform ID |
GPL29551 |
Series (1) |
GSE164103 |
Comparative transcriptomic analyses of high and low oleic acid content sunflower (Helianthus annuus L.) seed development |
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Relations |
BioSample |
SAMN17191186 |
SRA |
SRX9764193 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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