GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM8408792

Query DataSets for GSM8408792

Status

Public on Aug 16, 2024

Title

SL3

Sample type

SRA

Source name

leaf

Organism

Nicotiana benthamiana

Characteristics

tissue: leaf
cell line: leaf
cell type: leaf

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protoco
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About xxxxx raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2 2 . FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4 . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of sample
Differential expression analysis was performed using the DESeq2 5 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet gg
Based on the hypergeometric distribution, GO 6 , KEGG 7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software 8-9 . The anal used a predefined gene set, and the genes were ranked according to the degree of differentialexpression in the two types of samples.Then it is tested whether the predefined gene set wasenriched at the top or bottom of the rank
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM valued for each sample

Submission date

Jul 19, 2024

Last update date

Aug 16, 2024

Contact name

黄仁艳黄

E-mail(s)

[email protected]

Phone

18173172018

Organization name

湖南省农业科学院