Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Porcine Total RNA-Seq - Liver, Hypothalamus, LD Muscle

PROVIDER: PRJNA564815 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10095858_1.fastq.gz	Fastqsanger.gz
	SRR10095858_2.fastq.gz	Fastqsanger.gz
	SRR10095859_1.fastq.gz	Fastqsanger.gz
	SRR10095859_2.fastq.gz	Fastqsanger.gz
	SRR10095860_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

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.

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)

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 | E-GEOD-25923 | biostudies-arrayexpress

Folate deficiency during early-mid pregnancy affects the skeletal muscle transcriptome of piglets from a reciprocal cross

Project description:The objective of this study is to determine the effect of maternal folate deficiency on the skeletal muscle transcriptome of piglets from a reciprocal cross, in which full-sibling Landrace (LR) and full-sibling Chinese local breed Laiwu (LW) pigs were used for reciprocal cross matings, and sows were fed either a folate deficient or a normal diet during early-mid gestation. In addition, the difference in the responsiveness of the piglets to folate deficiency during early-mid pregnancy between reciprocal cross groups was investigated.Longissimus dorsi (LD) muscle samples were collected from newborn piglets and a 4 x 44K Agilent porcine oligo microarray was used for transcriptome analysis of porcine LD muscle. The results showed that folate deficiency during early-mid pregnancy affected piglet body weight, LD muscle fiber number and content of intramuscular triglyceride.

2013-10-14 | E-MEXP-3996 | 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)

2011-01-12 | GSE26382 | GEO

Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition from transcriptomic and proteomic profiles in Dingyuan pigs

Project description:we collected tissues of subcutaneous fat and longissimus dorsi (LD) muscle from individuals that have divergent of backfat thickness and intramuscular fat content, and have similar age and body weight. The transcriptomic and proteomic data were gained using RNA-Seq and TMT to identify the key genes and pathways that specifically regulate the subcutaneous fat and intramuscular fat deposition in Dingyuan pig.

2022-04-04 | PXD027061 | Pride

Project description:Porcine Mediobasal Hypothalamus RNA-Sequencing

| PRJNA982118 | ENA

Comparative transcriptome data of multi tissues in response to different environmental light-dark cycles

Project description:It is well known that host-microbes and immunity interactions are influenced by dietary patterns, as well as daily environmental light-dark (LD) cycles that entrain circadian rhythms in the host. Emerging data has highlighted the importance of diet patterns and timing on the interaction among circadian rhythms, gut microbiome, and immunity, however, their impacts on LD cycles are less reported. Therefore, we aim to study how LD cycles regulate the homeostatic crosstalk between gut microbiome, hypothalamic and hepatic circadian clock oscillations and immunity. We hypothesized that different environmental LD cycles: (1) constant darkness, LD0/24; (2) short light, LD8/16; (3) normal LD cycle, LD12/12; (4) long light, LD16/8; and (5) constant light, LD24/0, may affect immunity and metabolism to varying degrees. Therefore, 240 mice were managed with chow diets (CD) and antibiotics treatments (ABX) under five different LD cycles for 42 days. The liver (LIV), hypothalamus (HYP), inguinal white adipose tissue (iWAT), ileum epithelium (ILE), colon epithelium (COL), jejunum epithelium (JEJ), cecum epithelium (CEC), spleen (SPL), mammary gland (MAG), and thymus gland (THY) tissues were obtained for studying their impacts immunity using RNA-Seq data.

2023-03-10 | GSE226855 | GEO

High-throughput sequencing identifies miRNAs and their targets involved in porcine muscle development

Project description:To identify miRNAs involved in muscle development, three independent small RNA libraries from porcine skeletal muscle at the age of 63d、98d and 161d were constructed. A total of 4105184， 4606375 and 5113984 mappable small RNA sequences were generated in the three small RNA libraries, respectively, and 887 known and 472 new candidate miRNAs were obtained.

2017-02-10 | GSE64275 | GEO

miRNA expression in different tissues from different breeds of chicken

Project description:Affymetrix GeneChip miRNA Array was used to globally identify different expression miRNAs in hypothalamus, liver, breast muscle and abdominal fat between commercial broilers and indigenous chickens at seven-week old with hypertrophic pectoral muscle or normal pectoral muscle.

2016-09-01 | GSE80580 | 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