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Sample GSM5484384

Query DataSets for GSM5484384

Status

Public on Jul 11, 2022

Title

Wt, normal watering, time point ZT16 rep2

Sample type

SRA

Source name

seedlings

Organism

Arabidopsis thaliana

Characteristics

genotype: wt
ecotype: Columbia
protocol: normal watering, time point ZT16

Treatment protocol

Water deficit conditions were imposed as previously detailed (Riboni et al., 2013), so that under normal irrigation conditions plants grew under a Relative Soil Water Content (RSWC) of 80 – 90%, and 30% RSWC under water deficit conditions. RSWC was kept constant by daily weighing of pots and applications of water to maintain the desired value. Note that water defict was imposed soon after germination (i.e. in the short day) for each genotype and mantained throughout the experiment.

Growth protocol

In this study we used wild–type Arabidopsis plants, ecotype Columbia (Col–0) and mutant lines aba1-6 (Niyogi et al., 1998), gi-2 (Fowler et al., 1999). Seeds were germinated and plants grown in a controlled environment at a temperature of 21–23 °C, 65% relative humidity, either under long day (16 h light / 8 h dark) or short day (8 h light / 16 h dark) photocycles. Light was cool white fluorescent tubes (Osram, Sylvania) at a fluency of 120–150 μmol m-2 s-1 (Photosynthetically active radiation). Samples used for RNAseq analysis derived from an experiment previously described (Riboni et al., 2013). 3 week-old plants grown under short day conditions were moved to LD at Zeitgaber time (ZT) 8 (that is, at the end of the subjective day). Samples were harvested at ZT1, ZT8 (in the last short day) and ZT12 and ZT16 (the photo extension period). For each time point / treatment / genotype combination, we analyzed two biological replicates, each one consisting of approximately 50 seedlings pooled from three different Arabasket pots. To avoid soil carryover, we harvested only the aerial part of plants (i.e., above the hypocotyl).

Extracted molecule

polyA RNA

Extraction protocol

RNA was extracted using the Trizol reagent (Invitrogen). For RNA sequencing, RNA Quality Control was performed with an electrophoretic run on a Bioanalyzer instrument using the RNA 6000 Nano Kit (Agilent). RNA Integrity Number was determined, and all the samples were considered suitable for processing (RIN > 8). RNA concentration was estimated through a spectrophotometric measurement using a Nanoquant Infinite M200 instrument (Tecan).
Sequencing libraries were prepared using the TruSeq™ RNA Sample Preparation Kit (Illumina)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer IIx

Description

COL7c1

Data processing

Reads were mapped on the reference Arabidopsis thaliana genome (TAIR, version 10) using the bowtie2 program
Estimation of gene expression levels was performed using RSEM
Identification of differentially expressed genes was performed by the quasi-likelihood F-test as implemented by edgeR. False Discovery Rate (FDR) cut-off value of 0.05 was applied for the identification of significantly differentially expressed genes.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab delineated file with 48 rows and 26986 columns reporting the number of reads assigned to each gene

Submission date

Jul 29, 2021

Last update date

Jul 11, 2022

Contact name

Matteo Chiara

E-mail(s)

matteo.chiara@unimi.it

Organization name

University of Milan

Department

Biosciences