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Sample GSM6638228

Query DataSets for GSM6638228

Status

Public on Oct 01, 2023

Title

Col-0 -Pi #1

Sample type

SRA

Source name

Root

Organism

Arabidopsis thaliana

Characteristics

tissue: Root
ecotype: Col-0 ecotype
cell type: Root
genotype: wildtype
treatment: Minus Pi (-Pi)

Treatment protocol

The control condition was 1mM phosphate and the treated samples were grown without the addition of phosphate

Growth protocol

Arabidopsis seedlings were grown in 1/6MS agar plates for 7 days with or without phosphate

Extracted molecule

total RNA

Extraction protocol

RNA from roots was extracted using Promega ReliaPrep™ RNA Tissue Miniprep System
Illumina Sequencing library preparation

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013). Reads were aligned against Arabidopsis thaliana.TAIR10.39 genome using STAR (v. 2.5.3a, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Arabidopsis thaliana.TAIR10.39 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Reads were also aligned to the Arabidopsis thaliana.TAIR10.39 transcriptome using STAR (v. 2.5.3a, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Statistical analysis was performed for genes in R (R version 3.5.3). Genes with low counts were filtered out according to the rule of 1 count per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization and log-transformed into counts per million or CPM (EdgeR package version 3.24.3; Robinson et al. 2010). Differential expression was computed with limma-trend approach (Ritchie et al. 2015) by fitting all samples into one linear model. Moderated t-test was used for each contrast and F-test was used for interaction. For each group of comparisons, the adjusted p-value is computed by the Benjamini-Hochberg method, controlling for false discovery rate (FDR or adj.P.Val).
Assembly: TAIR10.39
Supplementary files format and content: Normalized expression values all genes. Excel file showing the normalize expression values for each gene in each replicate
Supplementary files format and content: Differential expression testing. Excel file showing the normalized expression value for each gene and the differential expression testing between genotypes and conditions

Submission date

Oct 14, 2022

Last update date

Oct 01, 2023

Contact name

JOAQUIN CLUA

Organization name

UNIL

Department

DBMV

Lab

YVES POIRIER