Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 32
Release date: Jan 24 2017
Last update date: Jun 21 2017
Access: Public
Computational protocol: FastQC, FASTX-Toolkit, TopHat, HTSeq, edgeR, JMP Pro
Dataset link Unique Genetic Responses Revealed in RNA-seq of the Spleen of Chickens Stimulated with Lipopolysaccharide and Heat

Experimental Protocol


At 22 days of age, divergent chicken breeds (Fayoumi and broiler) were treated with a thermal treatment (heat stress at 35C, or thermoneutral at 25C as a control) for 3.5 hours, then stimulated subcutaneously with an inflammatory stimulus (LPS, or saline as a control) for another 3.5 hours. Chickens were euthanized and spleens were harvested. A total of 32 indivudally coded cDNA libraries were prepared using TruSeq v2 library preparation kit which selects for polyA mRNA. In this 2x2x2 full factorial design with the factors of breed, thermal treatment, and inflammatory stimulus, there were a total of 8 treatment groups. Each treatment group had a total of 4 animal biological replicates. Therefore, a total of 32 individual barcoded samples were sequenced. A total of 8 individually barcoded cDNA libraries were sequenced per lane using the HiSeq Illumina 2500, and we used 4 lanes total. Reads were mapped to Galgal 2.0.

Repositories


GEO

GSE85434

ENA

SRP083322

BioProject

PRJNA340891

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Contact


Angelica Van Goor

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