GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM7880999

Query DataSets for GSM7880999

Status

Public on Sep 11, 2024

Title

Tobacco leaf tissue -GDH94×TN90_rep3

Sample type

SRA

Source name

hybrid GDH94×TN90

Organism

Nicotiana tabacum

Characteristics

tissue: mature leaf
line: GDH94×TN90

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM （http://deweylab.github.io/RSEM/）establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Assembly: Nitab-v4.5
Supplementary files format and content: TPM

Submission date

Nov 02, 2023

Last update date

Sep 11, 2024

Contact name

Renxiang Liu

E-mail(s)

rxliu@gzu.edu.cn

Organization name

Guizhou University

Street address

Huaxi