Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sus scrofa

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 (small RNA)

PROVIDER: PRJNA142489 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			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

Items per page:

1 - 5 of 6

Similar Datasets

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

Project description: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

| PRJNA136243 | ENA

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

Sus scrofa

Project description: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)

| PRJNA142279 | ENA

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

Transcription profiling of pig muscle longissimus dorsi sample of f2 animals, T-test paired and SAM

Project description:To identify biological processes as well as molecular markers for drip loss, the transcriptomes of logissimus dorsi from 6 sib pair of F2 animals Experiment Overall Design: 12 F2 animals of a resource population based on the breeds Duroc and Pietrain known to differ in meat quality and quantity traits were hybridized to Affymetrix Porcine Genome Arrays

2009-01-14 | E-GEOD-11193 | biostudies-arrayexpress

Gene expression data from Muscle Longissimus dorsi sample of F2 animals, T-test paired and SAM

Project description:To identify biological processes as well as molecular markers for drip loss, the transcriptomes of logissimus dorsi from 6 sib pair of F2 animals Keywords: T-test paired and SAM

2009-01-01 | GSE11193 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data