GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM8333748

Query DataSets for GSM8333748

Status

Public on Sep 01, 2024

Title

Tartary buckwheat,control,0 h-3

Sample type

SRA

Source name

seedings(leaf,stem)

Organism

Fagopyrum tataricum

Characteristics

tissue: seedings(leaf,stem)
cultivar: Dingku1
treatment: Hoagland's nutrient

Treatment protocol

Soak the seeds uniformly in water in a glass petri dish for about 2-3 days to germinate until the roots are 1-2 cm long, then transplant into soil or black hydroponic boxes for subsequent processing. When the Tartary buckwheat grows normally to the 2-leaf stage under long-day conditions. The Tartary buckwheat in the soil is treated with water shortage and drought for 10-14 days. The tartary buckwheat seedlings in the hydroponic box are treated with 20% PEG-6000 for 0 h, 2 h, 4 h, and 8 h.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
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 NovaSeq 6000

Description

P0-3

Data processing

The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using the DESeq2.
Assembly: PRJCA009237
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

Submission date

Jun 17, 2024

Last update date

Sep 01, 2024

Contact name

Qi Lu

E-mail(s)

luq2023@lzu.edu.cn

Organization name

lanzhou University

Street address

Tianshui South Road 222