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Sample GSM5655325

Query DataSets for GSM5655325

Status

Public on Jun 23, 2022

Title

GX100-2 3h root rep1

Sample type

SRA

Source name

root

Organism

Gossypium hirsutum

Characteristics

tissue: root
treatment: 150 mM NaCl
developmental stage: 3h

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from the roots of seedlings with an improved CTAB–ammonium acetate method (Zhao et al. 2012)
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TM-1 whole genome using HISAT v2.0 with default parameters.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Florea et al., F1000Res, 2013. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TM-1

Submission date

Oct 25, 2021

Last update date

Jun 23, 2022

Contact name

Anhui Guo

E-mail(s)

guoah@cau.edu.cn

Organization name

College of Agronomy and Biotechnology, China Agricultural University

Street address

College of Agronomy and Biotechnology,