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Sample GSM5093670

Query DataSets for GSM5093670

Status

Public on Aug 05, 2021

Title

CK_L1

Sample type

SRA

Source name

leaf, control

Organism

Gossypium hirsutum

Characteristics

treatment: none
tissue: leaf

Treatment protocol

300mM Na2SO4 and water at three true leaf stage for 12 h

Growth protocol

The cotton seedlings grew in normal sand, then transferred to Na2SO4 solution and water solution.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using TRlzol Reagent(Life technologies, California, USA) following the manufacturer's procedure. The integrity and concentration of total RNA was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). The isolated mRNA by NEB Next Poly (A) mRNA Magnetic Isolation Module (NEB, E7490) were used for constructing cDNA library through the manufacturer’s instructions of NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEB Next Multiplex Oligos for Illumina (NEB, E7500).
Approximately 200nt RNA inserts were used to synthesize the first-strand cDNA and the second cDNA, according to the fragmented mRNA. In the next step, the end-repair / dA-tail and adaptor ligation were performed for double-stranded cDNA, which is to form the cDNA library by Agencourt AMPure XP beads (Beckman Coulter, Inc.) and PCR amplification. Finally, the constructed cDNA libraries of the different samples were sequenced on a flow cell using an Illumina Novaseq 6000 platform.
The paired-end libraries was 300 bp ( ± 50 bp)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Using the Illumina paired-end RNA-seq approach
we aligned reads of all samples to the (http://mascotton.njau.edu.cn/info/1054/1118.htm) TM-1 reference genome using HISAT package
StringTie and edger was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with Fold Change ≥2 and FDR (false discovery rate) < 0.01 and statistical significance (p value < 0.05) by R package – edger.
Genome_build: TM-1 (http://mascotton.njau.edu.cn/info/1054/1118.htm)
Supplementary_files_format_and_content: 4_genes_fpkm_expression.xlsx

Submission date

Feb 19, 2021

Last update date

Aug 05, 2021

Contact name

Qinqin Wang

E-mail(s)

wang-1879@outlook.com

Phone

18790792020

Organization name

Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan 455000 China.