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Sample GSM5724896

Query DataSets for GSM5724896

Status

Public on Apr 01, 2022

Title

Acala SJ2 control replicate 3

Sample type

SRA

Source name

Root tissue (23 days-old-plants)

Organism

Gossypium hirsutum

Characteristics

treatment: Control (ctl)
genotype: Acala SJ2

Treatment protocol

Two treatments control (ctl) and root-knot nematode M. incognita infested (rkn). Control plants were not infested. For root-knot nematode (RKN) infestated plants, the roots of 12 days old seedlings of three genotypes NemX (resistant), SJ2 (susceptible) and WMJJ (moderately resistant) were infected with 5000 J2/plant RKN. The disease progression was noted for 10 days and infected roots from 23-day old plant were collected from each of the five plants, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extraction.

Growth protocol

Cotton plants were grown in a Greenhouse in pots with soil. Air temperatures in the greenhouse were maintained between 280 C and 350 C during the day and 240 C at night.

Extracted molecule

total RNA

Extraction protocol

The root samples from each genotype were grounded in liquid nitrogen, and total RNA was isolated three biological replicates following the manufacturer’s instructions using Spectrum TM Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). The yield and purity of RNA were analyzed with a ND-1000 Spectrophotometer (Nano Drop Technology, Wilmington, DE, USA). Only RNA samples with 1.8 - 2.2 ratio of absorbance 260/280 nm were used for analysis.
For each genotype, 2 mg of RNA from each of the three biological-replicates used for cDNA library preparation. The cDNA libraries were prepared following the TruSeq RNA Sample Preparation v2 low sample (LS) protocol guide (Illumina Inc., San Diego, CA USA)
Illumina Platform, MiSeq and HiSeq2500

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

RKN susceptible Genotype

Data processing

We first performed quality assessment of the resulting reads from the Illumina platform using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and processed sequencing libraries using Trimmomatic (version 0.39; ) to remove adapter read sequences.
We then quantified gene expression using the pseudo-alignment RNA-seq quantification program kallisto version 0.46.1. The G. hirsutum TM-1 UTx v2.1 genome release was used as a reference genome to align the reads (www.cottongen.org ; https://doi.org/10.1038/s41588-020-0614-5 )
We then integrated transcript-level abundances from kallisto to count-based statistical analysis in edgeR (version 3.13) to produce the table of read counts per locus.
Genome_build: The G. hirsutum TM-1 UTx v2.1 genome release was used as a reference genome to align the reads (www.cottongen.org ; https://doi.org/10.1038/s41588-020-0614-5 )
Supplementary_files_format_and_content: The table of counts is a tab-separated plaint text file (.txt) which contains the counts per million reads corresponding to each locus per library (rows), and each RNA-seq library sample (columns) is named according to genotype, condition and biological replicate (for example SJ2_ctl1 would be Acala SJ2-control conditions-replicate 1; rkn means root-knot nematode infested).

Submission date

Dec 08, 2021

Last update date

Apr 01, 2022

Contact name

Mauricio Ulloa

E-mail(s)

[email protected]

Phone

8063681659

Organization name

USDA-ARS