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Sample GSM1370252 Query DataSets for GSM1370252
Status Public on Apr 16, 2015
Title LR3
Sample type SRA
 
Source name 0.01 mg/l Roundup rep 3 liver
Organism Salmo trutta
Characteristics developmental stage: juvenile female
tissue: liver
treatment: 0.01 mg/l Roundup
Treatment protocol Fish were exposed to three concentrations of each chemical for 14 days using a flow-through system
Extracted molecule total RNA
Extraction protocol Liver samples were snap frozen with liquid nitrogen and stored at -80 C. Total RNA was extracted using Quiagen RNeasy columns
Libraries were constructed with Illumina TruSeq RNA sample preparation kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) was used to clip Illumina adapter sequences and to trim the first 12 bp at the 5’ end. 
Quality trimming of the 3' end of the reads using a sliding window trimmer was performed (http://wiki.bioinformatics.ucdavis.edu/index.php/Trim.slidingWindow.pl).
Digital normalisation using khmer (Brown et al. 2012, arXiv:1203.4802 [q-bio.GN]) was performed, and retained reads were paired using a custom script.
De novo transcriptome assembly was performed using Trinity (version R2013-02-25; (Grabherr et al. 2011))
Transcripts were annotated using Blast and all available Ensembl cDNA sequences for zebrafish (Danio rerio), medaka (Oryzias latipes), nile tilapia (Oreochromis niloticus), stickleback (Gasterosteus aculeatus), human and mouse (Release 71), RefSeq RNA, non-redundant nucleotides (nt) and proteins (nr) databases. Top hits with an e-value of < 1e-15 were retained. When no annotation could be found, the Trinity-generated transcript ID was given.
Sequence reads were mapped against the transcriptome assembly using Bowtie2 (version 2.1.0, (Langmead and Salzberg 2012)), using the -k 1 parameter. Count data was extracted using idxstats in samtools (version 0.1.18, (Li et al. 2009)) and differential expression analysis was conducted in edgeR (Robinson et al. 2010).
Genome_build: n/a
Supplementary_files_format_and_content: The edgeR results file for each treatment group versus the control group was merged with the annotation results, and is provided in a tab delimited text file. For each transcript raw count data for each replicate is included together with the log fold change, P values and FDR values from the expression analysis for that treatment.
 
Submission date Apr 16, 2014
Last update date May 15, 2019
Contact name Tamsyn Uren Webster
E-mail(s) T.M.UrenWebster@swansea.ac.uk
Organization name Swansea University
Street address Wallace Building
City Swansea
ZIP/Postal code SA2 8PP
Country United Kingdom
 
Platform ID GPL18582
Series (1)
GSE56855 Transcript profiles of juvenile female brown trout exposed to glyphosate and Roundup herbicides.
Relations
BioSample SAMN02728971
SRA SRX518756

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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