U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX3547092: GSM2918403: Col-0 DMSO rep1; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 16.1M spots, 1.2G bases, 492Mb downloads

Submitted by: NCBI (GEO)
Study: Transcriptome analysis of isoxaben-induced loss of cell wall integrity in Arabidopsis seedling liquid culture
show Abstracthide Abstract
Plant cells are surrounded by walls, which must often meet opposing functional requirements during plant growth and defense. The cells meet them by modifying wall structure and composition in a tightly controlled and adaptive manner. The modifications seem to be mediated by a dedicated cell wall integrity (CWI) maintenance mechanism. Currently the mode of action of the mechanism is not understood and it is unclear how its activity is coordinated with established plant defense signaling. We investigated both the responses to cell wall damage (CWD) compromising CWI and the underlying mechanism in Arabidopsis thaliana. A cellulose biosynthesis inhibitor isoxaben was used as a tool to induce the loss of cell wall integrity. Isoxaben was chosen because it only affects a certain cell type / differentiation stage, and weakens the cell walls indirectly by inhibiting a biosynthetic process, making CWD occurrence dependent on high turgor levels (allowing simultaneous manipulation of the responses by addition of osmotica like sorbitol, mannitol, etc.). Isoxaben treatment causes structural damage, induction of lesion formation, cell death, deposition of lignin and callose as well as production of jasmonic acid and salicylic acid. Isoxaben-resistant mutant ixr1-1 is included to ensure the specificity of the treatment. Overall design: Both genotypes (Col-0 and ixr1-1) were treated with either isoxaben or DMSO (mock). Three replicates of each sample were analyzed.
Sample: Col-0 DMSO rep1
SAMN08335958 • SRS2821299 • All experiments • All runs
Library:
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNA was extracted using a Spectrum Plant Total RNA Kit (Sigma-Aldrich). RNA concentration was measured using a Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and integrity assessed using a Agilent RNA 6000 Pico Kit. RNA Seq libraries were prepared using a TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer's instructions. 500 ng total RNA was used as starting material.
Experiment attributes:
GEO Accession: GSM2918403
Links:
Runs: 1 run, 16.1M spots, 1.2G bases, 492Mb
Run# of Spots# of BasesSizePublished
SRR645639216,050,1901.2G492Mb2018-01-12

ID:
4927921

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...