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RNA-Seq results of six Chinese Sutai piglets from ear tissue based on Illumina HiSeq 2000 platform

ABSTRACT: Purpose: The paired-end sequencing strategy of RNA-Seq improves sequencing efficiency and extends short read lengths for better understanding pig transcriptome. The goals of this study are to identify whether alternative splicing sites or alternative 3' gene boundary caused by a CNV located in 3' region of MSRB3 gene and find differential expression genes in ear tissue between QQ and qq genotype piglets for QTL of ear size Methods: Ear tissue mRNA profiles of 6 piglets including 3 QQ and 3 qq genotypes responsible for QTL of ear size were generated by deep sequencing, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 93.6-95.3 million 2 x 90 bp paired-end clean reads per sample to the pig genome (Sscrofa 10.2) and identify 19,819-20,136 annotated genes in each sample. Our ranking analysis identified a list of 281 differentially expressed genes with a >1 fold change at a false discovery rate lower than 0.001. But we found no alternative transcripts and differential expression of MSRB3 gene. Conclusions: In our study, the expression levels of MSRB3 gene had no significant difference in the ear tissue between QQ and qq individuals, and no alternative splicing was found for MSRB3 gene between QQ and qq individuals.

ORGANISM(S): Sus scrofa

PROVIDER: GSE80613 | GEO | 2016/04/26

SECONDARY ACCESSION(S): PRJNA319492

REPOSITORIES: GEO

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Project description:Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress.To further investigate the different breed-specific metabolic characters, a comparison of gene expression profile in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six niemblegen 135K expression microarrays were used. Among 44,987 pig transcripts investigated, 23,807 transcripts retained for further analysis after removing the probes with poor quality intensities and low dependability.All these qualified transcripts were then annotated by manual blast and by referring to previously developed protein-based annotation for pigs. In total, we observed 9,447 genes expressed in the liver of new born piglets. The microarray data of LW piglets were treated as control in the selection of differentially expressed genes related to EHL piglets. The FDR (False Discovery Rate) and fold change were calculated by SAMR 3.02. With FDR< 5%, after the removal of redundant and unannotated sequences, 53 genes were found to be significantly up-regulated and 200 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. With FDR < 10%, 298 genes were found to be significantly up-regulated and 510 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs. Six newborn male piglets were sampled from three litters (2 from each litter) of purebred EHL and LW sows and sacrificed. Liver samples were immersed in liquid nitrogen immediately after collection and then stored at -70 M-BM-0C. Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturerM-bM-^@M-^Ys instructions. Total RNAs of the two littermate piglets were pooled for the microarray analysis. The pooled samples were named as EHL1-3 and LW1-3, representing 3 mixed liver RNA samples each from EHL and LW piglets, respectively. Microarray experiment was performed by a service provider (CapitalBio, Beijing, China). The microarray (Probe length 60-mer, 135K Format) containing 44987 probe sets was provided by Roche-NimbleGen.

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RNA-Seq results of six Chinese Sutai piglets from ear tissue based on Illumina HiSeq 2000 platform

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