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Sample GSM4547179

Query DataSets for GSM4547179

Status

Public on Sep 14, 2020

Title

FG1817_08

Sample type

SRA

Source name

exercised eels_ED

Organism

Anguilla anguilla

Characteristics

swimming exercise: exercised
swimbladder functional/non-functional: damaged, non-functional swimbladders (ED)
tissue: gas gland tissue
cell type: swimbladder gas gland cells

Treatment protocol

Two weeks prior to the experiments, the salinity was increased to 35 PSU. Eels were transferred to the swim tunnel and acclimatized to the new environment at a pressure of 1 bar and a flow rate of 0.1 m s-1 for 2 h at a temperature of 14°C. Over a period of 16 h, eels were acclimatized to higher flow rates of up to 0.5 bl s-1, which corresponds to the estimated swimming speed of the spawning migration. Pressure was elevated at a rate of 1 bar min-1 which corresponds to the natural diving speed of 0.15 m s-1 to finally 8 bar. The 24 h experiment was terminated by 8 h of exercise at a velocity of 0.5 bl s-1 and a pressure of 8 bar (= 0.8 MPa). At the end of the experiment, pressure was reduced to atmospheric pressure at a rate of 1 bar min-1 and water velocity was reduced to 0.1 m s-1. Eels were removed from the tunnel, immediately anesthetized with 2-phenoxyethanol (1 ml l-1), and subsequently decerebrated and spinally pithed. The swimbladder was dissected and the epithelium, consisting of gas gland cells, was carefully freed from connective tissue. The epithelium was transferred into RNAlater™ solution and stored at -80oC until further use.

Growth protocol

European eels were caught by local fishermen and kept in freshwater for a few days.

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated from gas gland tissue using the Qiagen miRNeasy kit. Quality and integrity of the RNA waere checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip.
Illumina RNASeq libraries were prepared from 0.5 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

FG1817_08_34089_S12_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx

Data processing

Illumina NovaSeq6000 RTA3 software used for basecalling: version 3.4.4
For comparison between FG1924 and FG1817, all forward reads were trimmed to a final size of 50 nt using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html)
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) using TopHat (version 2.0.13) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 1.9) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9) (Anders et al., 2015)
Differentially expressed genes were identified using DESeq version 1.34.1 (run in R version 3.5.2) (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Anguilla_anguilla_genome_v1_09_nov_10
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj; sample x; Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component

Submission date

May 11, 2020

Last update date

Sep 14, 2020

Contact name

Gabriel Schneebauer

Organization name

University of Innsbruck

Street address

Technikerstrasse 25

City

Innsbruck