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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