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Sample GSM2455327 Query DataSets for GSM2455327
Status Public on Jul 18, 2017
Title TruSeq met1 Rep2
Sample type SRA
Source name Inflorescence tissue
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype/variation: met1
rna type: total RNA
library type: TruSeq
Growth protocol Arabidopsis thaliana plants were grown on soil in a growth chamber at 22°C for two weeks in a 12h/12h light cycle and then transferred to a 16h/8h light cycle.
Extracted molecule total RNA
Extraction protocol RNA was extracted from inflorescence tissue using the TRIzol extraction method.
To generate total RNA-seq libraries, RNA was subjected to ribodepletion with Ribo Zero (Illumina) and libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). RNA 3’end libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) adjusted for longer insert lengths by diluting the second strand synthesis buffer with water in a ratio 1:1. sRNA-seq libraries were constructed by Fasteris SA. Libraries were prepared using the Illumina TruSeq Kit SBS v3.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description met1_total2
Data processing Illumina Casava1.8 software used for basecalling.
Trimming of reads with Trimmomatic-0-2.36 using the following parameters: SLIDINGWINDOW:4:10 AVGQUAL:20 MINLEN:50
Mapping to Arabidopsis genome (TAIR10) with STAR (--outFilterMultimapNmax 50 --outFilterMatchNmin 30 --alignSJoverhangMin 3 --alignIntronMax 10000)
Read counting with Rsubread (allowMultiOverlap=T, isPairedEnd=T, strandSpecific=2, countMultiMappingReads=T)
Read normalization with edgeR.
sRNA libraries were trimmed with Trimmomatic-0-2.36 using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15
sRNA counting was performed using the function of the ncPRO-seq v1.5.1 pipeline.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_CPM.txt: Tab-delimited text files of count per million (CPM) values.
Supplementary_files_format_and_content: met1_sRNA_processed.txt: Tab-delimited text file of counts per sRNA species.
Submission date Jan 13, 2017
Last update date May 15, 2019
Contact name Stefan Oberlin
Organization name ETH Zürich
Department Department of Biology
Street address Universitätstrasse 2
City Zürich
ZIP/Postal code 8092
Country Switzerland
Platform ID GPL17639
Series (1)
GSE93584 A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
BioSample SAMN06227256
SRA SRX2488472

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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