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Sample GSM4547182 Query DataSets for GSM4547182
Status Public on Sep 14, 2020
Title Sample 6_IL-14-12_6 [re-analysis]
Sample type SRA
 
Source name unexercised eels (SC)
Organism Anguilla anguilla
Characteristics swimming exercise: unexercised
tissue: gas gland tissue
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 IL-14-12_6_CTTGTA_L000
This is duplicated sample record of GSM2730543 for the convenient retrieval of the complete raw data from SRA
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
ZIP/Postal code 6020
Country Austria
 
Platform ID GPL20640
Series (1)
GSE150340 Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel
Relations
Reanalysis of GSM2730543
BioSample SAMN14891936
SRA SRX8326530

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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