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Sample GSM5903353 Query DataSets for GSM5903353
Status Public on Jan 06, 2023
Title CC_T_A
Sample type SRA
 
Source name CS0 T+
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: seedling
age: 9 days
genotype: wild-type
treatment: Tenofovir 10uM
treatment: not stressed
Treatment protocol In drug treated plants, Tenofovir (Cayman Chemical, N 13874), was dissolved in DMSO and added to the medium at 10 µM. One-week old seedlings have been primed by cold treatment for 24°C and immediately transferred to normal growth conditions (Control plants or CS) or to 37°C for 24hr (Heat Stressed or HS) plants. Plants have been collected 24h after heat application (HS0). Tenofovir-treated and control Arabidopsis plants have been subsequently grown at 21°C for the remaining time, and samples have been collected 3 days after heat-stress.
Growth protocol Arabidopsis seedlings were grown in plates on ½ MS media (1% sucrose and 0.8% agar, pH5.7) at 20°C under 12h light conditions (12h light/12h dark)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from seedlings using the RNeasy Plant Mini Kit (Qiagen), following the manufacturer's instructions. The RNA quality and integrity were assessed on the Agilent 2200 Tape Station.
Libraries for RNA expression analysis were prepared in tripicate from 1 µg of high-integrity total RNA (RIN>8) using the TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA) following the manufacturer’s instructions. Libraries quality and fragment sizes were checked with a TapeStation 2200 (Agilent technologies, Santa Clara, CA) instrument.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description control with Tenofovir rep1
Data processing Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
The cleaned reads were mapped to Arabidopsis reference genome (TAIR10 version) by TopHat2 (Kim et al., 2013).
Picard tools (available from http://broadinstitute.github.io/picard/) was used to discard duplicated reads.
Mapped reads from TopHat2 analysis were subsequently counted using htseq-count (Anders et al., 2015), and the raw count per gene was used to determine differentially expressed genes between control and Tenofovir-treated samples using DESeq (Anders and Huber, 2010) and default parameters. Genes with a significance p-value below 0.05 after Benjamini and Hochberg correction were considered to be differentially expressed
Genome_build: TAIR10
Supplementary_files_format_and_content: For each genotype, the bigwig coverage file is provided, generated with samtools depth (Li et al 2009, Bioinformatics) from the the aligned reads.
 
Submission date Feb 16, 2022
Last update date Jan 08, 2023
Contact name Marco Catoni
Organization name University of Birmingham
Department School of Biosciences
Street address Edgbaston
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platform ID GPL19580
Series (1)
GSE196869 The application of a reverse transcriptase inhibitor suppresses LTR retrotransposon mobilization in plants [RNA-seq]
Relations
BioSample SAMN25996618
SRA SRX14203732

Supplementary file Size Download File type/resource
GSM5903353_CC_T_A.bw 65.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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