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Sample GSM5685376 Query DataSets for GSM5685376
Status Public on Nov 01, 2024
Title Sp18Ah1
Sample type SRA
 
Source name spleen
Organism Anguilla anguilla
Characteristics tissue: spleen
treatment: infection of A. hydrophila at 18hpi
Treatment protocol Prior to the experiment, fish were reared in 1000-L plastic tanks with fresh water and a normal diet (48 % protein and 5.6 % fat) for one week, and then randomly distributed into 6 aquariums (55 cm ¡Á 40 cm ¡Á 30 cm) with 25 fish in each aquarium. Each experimental fish in 3 groups (Infection group) was intraperitoneally injected with 100 ¦ÌL of A. hydrophila suspension (1 ¡Á 108 CFU/mL in PBS), and each control fish in 3 groups (Control group) injected with the same volume of PBS. The fish were not feed during the challenge experiment, with the water temperature at 25 ¡À 1¡ãC.
Growth protocol European eels (n = 150) with a mean body mass of 50 g were obtained from Zhangpu, Fujian province of China.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the TRIzol? Reagent (ThermoFisher Scientific, Massachusetts, USA) according to the manufacturer's protocol.
The mRNA-seq library construction was performed with the TruseqTM RNA sample prep Kit (Illumina, California, USA ) following the manufacturer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Raw reads were produced by an Illumina Hiseq4000 instrument with 150 bp paired end reads by the BioMarker Biotechnology Co., Ltd (Beijing).
The trimming and quality controls of raw Illumina reads were performed using Sickle (https://github.com/najoshi/sickle) and SeqPrep (https://github.com/jstjohn/SeqPrep) with the default settings.
Raw data reads in fastq format were initially processed using in-house perl scripts.
Genome_build: none
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Nov 10, 2021
Last update date Nov 01, 2024
Contact name cao lu
E-mail(s) caolu@ihb.ac.cn
Phone +8618202736768
Organization name Institute of Hydrobiology
Department Chinese Academy of Sciences
Street address 7 Donghu South Road
City Wuhan
State/province Hubei
ZIP/Postal code 430072
Country China
 
Platform ID GPL24544
Series (1)
GSE188550 Time-resolved and multi-tissue RNAseq provided new insights on the immune responses of European eels following infection with Aeromonas hydrophila
Relations
BioSample SAMN23033231
SRA SRX13097150

Supplementary file Size Download File type/resource
GSM5685376_Sp18Ah1.txt.gz 640.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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