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Sample GSM1705286 Query DataSets for GSM1705286
Status Public on May 27, 2016
Title flooding_no3
Sample type SRA
 
Source name leaf_flooding_no insect
Organism Solanum dulcamara
Characteristics water treatment: flooding
insect treatment: no
tissue: leaf
Treatment protocol 5 days water treatments + 2 days insect treatments, water treatments were maintained during insect treatments
Growth protocol plants were grown in standard greenhouse
Extracted molecule total RNA
Extraction protocol Total RNA of the following tissues was isolated with the Plant RNeasy kit (Qiagen). DNase treatment done using TURBO DNA-free kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description processed data column: 45
Data processing read mapping by bowtie v. 0.12.7
Global normalization among samples was performed by the method implemented in the R-package DESeq
Reads per kilobase of contig length per million mapped reads (RPKM) values were also calculated and used to filter out noise contigs with RPKM lower than 1 in all samples
Differential expression calls, based on normalized read counts, were performed using the DESeq
false discovery rate (FDR) p values calculated according to the Benjamini & Hochberg procedure
Genome_build: Solanum dulcamara transcriptome DAgostino2013 Contigs, solgenomics.net
Supplementary_files_format_and_content: each file is a matrix of contig numbers and their raw (or normalized) read counts in each sample
 
Submission date Jun 08, 2015
Last update date May 15, 2019
Contact name Duy Nguyen
E-mail(s) nguyenmduy@gmail.com
Phone +31611377444
Organization name Radboud University
Department Molecular Plant Physiology
Street address Heyendaalseweg 135
City Nijmegen
ZIP/Postal code 6525AJ
Country Netherlands
 
Platform ID GPL20294
Series (1)
GSE69648 Effects of Drought and Flooding on Herbivore-Triggered Transcriptomic Response in Solanum dulcamara
Relations
BioSample SAMN03764708
SRA SRX1053397

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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