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Sample GSM3690688 Query DataSets for GSM3690688
Status Public on May 07, 2019
Title Col0-3
Sample type SRA
 
Source name seedlings
Organism Arabidopsis thaliana
Characteristics tissue: seedlings
developmental stage: 10 day old seedlings
background strain: Col-0
genotype: Wildtype
treatment: untreated
Treatment protocol Seedling were untreated
Growth protocol Arabidopsis thaliana plants were grown on 0.8% Murashige and Skoog (MS) agar for 10 days. Plants were grown at 20°C under 16h day/8 h night photoperiod.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the ReliaPrep™ RNA Tissue Miniprep System (Promega) and processed as per manufacturer’s instructions.
Libraries were prepared using the Illumina Truseq stranded mRNA sample preparation kit, according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Fastq files were aligned to Arabidopsis genome (Arabidopsis Araport 2017) using STAR
BAM files resulting from the alignments were summarized to genes using the HTSeq package
Expression data was normalized using the DESeq package from bioconductor in R
Differentially expressed genes (³2-fold and £5% false discovery rate) were identified using the DESeq package
Genome_build: Arabidopsis thaliana genome (Arabidopsis Araport 2017)
Supplementary_files_format_and_content: Tab-delimited text files include log2 counts per million (CPM) values for each sample
 
Submission date Mar 28, 2019
Last update date May 07, 2019
Contact name Paul William Denny
E-mail(s) p.w.denny@durham.ac.uk
Phone 01913343983
Organization name Durham University
Department Biosciences
Street address Lower Mountjoy
City Durham
State/province Durham
ZIP/Postal code DH1 3LE
Country United Kingdom
 
Platform ID GPL19580
Series (1)
GSE129016 Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana
Relations
BioSample SAMN11282530
SRA SRX5590301

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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