|
| Status |
Public on Aug 04, 2017 |
| Title |
Sample 17_IL-14-12_17 |
| Sample type |
SRA |
| |
|
| Source name |
yellow eel_uninfected
|
| Organism |
Anguilla anguilla |
| Characteristics |
developmental stage: yellow eel
infection status: uninfected
tissue: swimbladder; gas gland tissue
|
| Treatment protocol |
Prior to dissection, animals were either killed with an overdose of tricaine methanosulfonate or anesthetized with tricaine methanosulfonate and subsequently decerebrated. The swimbladder was dissected, freed from connective tissue to reveal the actual gas gland tissue, immediately shock frozen in liquid nitrogen and stored at -80°C until futher 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 2 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 |
processed data: DESeq_yellow_uninfected_vs_yellow_infected.xlsx
|
| Data processing |
Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) using TopHat (version 2.0.5) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 0.1.18) (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 (Anders et al., 2015)
Differentially expressed genes were identified using DESeq (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; Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component; Transcripts; Longest transcript length; Total length; sample x; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj
|
| |
|
| Submission date |
Aug 03, 2017 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE102221 |
Effects of an Anguillicola crassus infection on steady-state mRNA levels in gas gland tissue of the European eel |
|
| Relations |
| BioSample |
SAMN07446915 |
| SRA |
SRX3058374 |
