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Sample GSM4404566

Query DataSets for GSM4404566

Status

Public on May 18, 2021

Title

XBDR3

Sample type

SRA

Source name

Root

Organism

Spinacia oleracea

Characteristics

cultivar: Bloomsdale
tissue: Root
oxalate content: Low Oxalate

Growth protocol

Spinach varieties; Bloomsdale and USDA accession PI175311 were selected for the study. The seeds of both varieties were grown in an environmentally controlled growth chamber at the Texas A&M AgriLife Research and Extension Center in Uvalde, Texas, in plastic containers using Turface () as a growing medium. Plants were grown in 200 μmol·m-2·s -1 for 12 h.at 23°C. The plants were fertilized with with Peter’s professional mix (5-11-26) (0.974 g/L) and nitrogen level was mainatained at 200 ppm with addition of calcium Nitrate (Ca(NO3)2). Each treatment had six independent containers, each with independent plants. Plant samples from 6-week old plants were frozen in liquid nitrogen and stored at −80 °C until subsequent analyses. Three independent plants were used for oxalate analysis, total RNA extractions and physiological analysis.

Extracted molecule

total RNA

Extraction protocol

The flash-frozen plant samples in liquid nitrogen were ground to a fine powder using a paint shaker (Harbil, Wheeling, IL, USA) and 3-mm-diameter steel balls (Abbott Ball, West Hartford, CT, USA). Total RNA was extracted using an RNeasy® Plant Mini Kit (QIAGEN Sciences, Germantown, MD, USA) as per the manufacturer’s protocol and treated with DNase1 (QIAGEN Sciences, Germantown, MD, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Spinacia_oleracea whole genome using hisat2-2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts
Differeantial expression analysis with DEseq2
Genome_build: Spinacia_oleracea V1.0
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

Submission date

Mar 10, 2020

Last update date

May 18, 2021

Contact name

Vijay Joshi

E-mail(s)

vijay.joshi@tamu.edu

Phone

8302789151

Organization name

Texas A&M AgriLife Research