Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 4
Release date: Oct 26 2010
Last update date: Nov 27 2017
Access: Public
Diseases: Salmonella Infections
Dataset link Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection

Experimental Protocol


Zebrafish embryos were infected with Salmonella typhimurium (strain SL1027) by microinjection of DsRED-labeled bacteria into the caudal vein close to the urogenital opening after the onset of blood circulation (27 hpf). An equal volume of PBS was injected in the control group. RNA samples were collected at 8 hours post infection (hpi) and samples from triplicate infection experiments were pooled. DGE libraries from the RNA pools (1 μg) of Salmonella-infected and control embryos were prepared using the DGE:Tag Profiling for NlaIII Sample Prep kit from Illumina as previously described (Hegedus et al., 2009). The libraries were sequenced in duplicate using 2 (Control 1; Salmonella infected 1) and 3 pmol (Control 2; Salmonella infected 2) of cDNA. Sequencing was performed using the Illumina Genome Analyzer II System (BaseClear B.V., Leiden, The Netherlands) according to the manufacturer’s protocols. Image analysis, base calling, extraction of 17 bp tags and tag counting were performed using the Illumina pipeline. Tag counts from duplicate libraries were merged in silico.

Repositories


GEO

GSE22472

ArrayExpress

E-GEOD-22472

ENA

SRP002676

BioProject

PRJNA128589

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Contact


Oliver Stockhammer