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A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing

ABSTRACT: A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing

PROVIDER: PRJNA136243 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR080697.fastq.gz	Fastqsanger.gz
	SRR080698.fastq.gz	Fastqsanger.gz
	SRR080699.fastq.gz	Fastqsanger.gz
	SRR080700.fastq.gz	Fastqsanger.gz
	SRR080701.fastq.gz	Fastqsanger.gz

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A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (small RNA)

Project description:Pig is the important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-seq) to generate a high-resolution map of the porcine miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from a F2 female full-sib pair with extreme phenotypes on growth and fat deposit. Through small RNA sequencing and on the basis of miRbase15.0, we detected a total of 184 mature miRNAs and 164 unique porcine novel miRNAs. Some conserved miRNAs, such as miR-122, miR-1, miR-206 and let-7 family showed high expression level in this study. Finally, we identified 10, 20 and 63 differentially expressed miRNAs, respectively, in LI, LD and AF. This high resolution and comprehensive transcriptome analysis significantly enhances the current genome annotation of pigs. examining the complexity of pig transcriptome in three organs from a female full-sib pair

2010-12-20 | E-GEOD-25923 | biostudies-arrayexpress

A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA)

Project description:Pig is an important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-Seq) to generate a high-resolution map of the porcine transcriptome and miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from an F2 female full-sib pair with extreme phenotypes in growth and fat deposit. On the basis of the porcine annotated genes against the UCSC database, we identified 21,414 annotated genes in our RNA-Seq analysis and 48,045-122,931 novel transcript fragments, which could be clustered into 17,085-29,499 novel transcriptional active regions (nTARs). We found that ~18.8% of the detected known genes showed alternative splicing patterns, and alternative 3’ splicing was the most common type of alternative splicing events in pigs. We also detected that more than 22.7% of the known genes identified here were extended at their 5’ and/or 3’ end. We identified 2,796, 1,551 and 835 differentially expressed genes (DEGs), respectively, in AF, LI and LD between the two individuals. Examining the complexity of the pig transcriptome in three organs (liver, abdominal fat, longissimus dorsi muscle) from a female full-sib pair.

2011-01-12 | E-GEOD-26382 | biostudies-arrayexpress

A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (small RNA)

2010-12-20 | GSE25923 | GEO

A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA)

2011-01-12 | GSE26382 | GEO

A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing

Project description:This SuperSeries is composed of the SubSeries listed below.

2011-01-12 | GSE26572 | GEO

Human subcutaneous adipose tissue gene expression (SOS Sib-pair study, offspring cohort)

Project description:Obesity has considerable effects on morbidity and mortality, and the prevalence of obesity has been increasing rapidly worldwide during the past two decades. Even if obesity affects the entire individual, adipose tissue plays a central role in the development of obesity. Expression profiling of adipose tissue may give insights into the mechanisms contributing to obesity and obesity-related disorders. The Swedish Obese Subjects (SOS) Sib-Pair Study consists of 154 nuclear families with BMI-discordant sib pairs (BMI difference more than 10 kg/m2) resulting in a study population consisting of 732 subjects. The full SOS Sib-Pair study offspring cohort consists of 425 subjects. Microarray expression analysis in subcutaneous adipose tissue was performed in 375 subjects (262 women and 113 men) of the SOS Sib-Pair offspring cohort.

2013-01-22 | GSE27916 | GEO

Human subcutaneous adipose tissue gene expression (SOS Sib-pair study, offspring cohort)

2013-01-22 | E-GEOD-27916 | biostudies-arrayexpress

A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing.

Project description:BackgroundElucidation of the pig transcriptome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits such as fat deposition, metabolism and growth.ResultsHere we used massive parallel high-throughput RNA sequencing to generate a high-resolution map of the porcine mRNA and miRNA transcriptome in liver, longissimus dorsi and abdominal fat from two full-sib F2 hybrid pigs with segregated phenotypes on growth, blood physiological and biochemical parameters, and fat deposition. We obtained 8,508,418-10,219,332 uniquely mapped reads that covered 78.0% of the current annotated transcripts and identified 48,045-122,931 novel transcript fragments, which constituted 17,085-29,499 novel transcriptional active regions in six tested samples. We found that about 18.8% of the annotated genes showed alternative splicing patterns, and alternative 3' splicing is the most common type of alternative splicing events in pigs. Cross-tissue comparison revealed that many transcriptional events are tissue-differential and related to important biological functions in their corresponding tissues. We also detected a total of 164 potential novel miRNAs, most of which were tissue-specifically identified. Integrated analysis of genome-wide association study and differential gene expression revealed interesting candidate genes for complex traits, such as IGF2, CYP1A1, CKM and CES1 for heart weight, hemoglobin, pork pH value and serum cholesterol, respectively.ConclusionsThis study provides a global view of the complexity of the pig transcriptome, and gives an extensive new knowledge about alternative splicing, gene boundaries and miRNAs in pigs. Integrated analysis of genome wide association study and differential gene expression allows us to find important candidate genes for porcine complex traits.

| S-EPMC3188532 | biostudies-literature

Kin recognition: neurogenomic response to sib mating avoidance in a parasitic wasp

Project description:Sib mating increase homozygosity and can lead to inbreeding depression. Selective pressures have favored the evolution of kin recognition and sib avoidance in mate choice. Such avoidance behavior has been recorded in the parasitoid wasp Venturia canescens where the sex determining system (single-locus complementary sex determination, sl-csd) introduces an extra short-term cost to inbreeding; females preferentially mate with unrelated males. The genetics underlying mate choice of females and kin recognition remains largely unexplored. Here we analyzed the head transcriptomic changes after exposure to distinct stimulus: courtship by unrelated male or courtship by brother, while transcriptome of females alone was used as control. Our results demonstrate that male courtship provokes a major transcriptome reprogramming in females heads. The transcriptomic response is highly dependent on the compatibility of the courting male. We subdivided the socially responsive genes using an integrative gene network analysis, we highlighted genes regulated by courtship, whatever the relatedness of the courting male. We also showed that the regulation of some peculiar group of genes is very specific of compatible male courtship, while others are regulated only by incompatible male courtship. We suggest that those different transcriptomic responses lead to mating decision or sib mating avoidance behavior observed in this species.

2018-12-20 | GSE124129 | GEO

The Impact of Patient Complexity on Healthcare Utilization

Project description:Healthcare providers are routinely being assessed for metrics designed to assess the quality of the care they deliver. There is growing consensus that these measurements, which typically assess the percentage of patients meeting a specific standard of care, should be adjusted for the clinical complexity of the providers. This study will assess whether adjusting for the social complexity of the patient panel adds significantly to adjustment for clinical complexity in explaining apparent differences in quality of care provided by Primary care providers and clinics.

| 2257794 | ecrin-mdr-crc

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