Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs

ABSTRACT: Cells are the functional intermediaries linking genotypes to phenotypes. However, the systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation of complex phenotypes are still understudied in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell atlas of adult pigs that encompasses 229,268 high-quality nuclei from 19 tissues. We further deconvolute bulk RNA-seq samples from 17 matching tissues in the PigGTEx project, dissecting thousands of genetic variants with cell-type interaction effects on gene expression (ieQTL) . Additionally, We colocalize ieQTL with variants associated with 268 complex traits.

ORGANISM(S): Sus scrofa domesticus

PROVIDER: GSE233285 | GEO | 2025/06/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-altitude Adaptation of Tibetan Pigs

Project description:To elucidate further molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes in Tibetan pigs, we used transcriptome microarrays from lung tissues of Tibetan pigs and Duroc pigs both at high and low altitude analyzed differentially expressed genes (DEGs), biological pathway and constructed co-expression regulation network. A total of 3,068 DEGs were identified which involved metabolic process, cellular process, immune biological process and angiogenesis pathway. The regulatory (RIF) and phenotypic (PIF) impact factors analysis identified several known and potentially regulators of hypoxia adaption, including IKBKG, KLF6 and RBPJ (RIF1), SF3B1, EFEMP1, HOXB6 and ATF6 (RIF2).

2016-07-15 | GSE84409 | GEO

Integrating multi-omics data to identify key functional variants affecting feed efficiency in pigs

Project description:Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key functional variants associated with feed efficiency in pigs. Identification of differentially expressed genes in the duodenal and muscle tissues of low- and high-FCR pigs revealed that pathways related to digestion of dietary carbohydrate are responsible for differences in feed efficiency between individuals. Differential open chromatin regions identified by ATAC-seq were linked to genes involved in glycolytic and fatty acid processes. GWAS identified 211 significant single nucleotide polymorphisms associated with feed efficiency traits, with candidate genes PPP1R14C, TH, and CTSD. Integration of duodenal ATAC-seq data and GWAS data identified six key functional variants, particularly in the 1500985–1509676 region on chromosome 2. In those regions, CTSD was found to be highly expressed in the duodenal tissues of pigs with a high feed conversion ratio, suggesting its role as a potential target gene. Overall, the integration of multi-omics data provided insights into the genetic basis of feed efficiency, offering valuable information for breeding more efficient pig breeds.

2024-09-30 | GSE270124 | GEO

Massively Parallel Reporter Assay of human-specific substitutions in neurodevelopmental enhancers

Project description:We performed a Massively Parallel Reporter Assay (MPRA) to screen >30,000 human-specific substitutions in ChIP-seq-identified Human Gain Enhancers (HGEs) and Human Accelerated Regions (HARs), highly conserved non-coding regions that show accelerated sequence evolution in humans. After comparing human and chimpanzee reference alleles, we used a second MPRA to deconvolute individual substitutions within differentially active enhancers from substitutions in the same fragment and from other variants (human segregating variants or chimpanzee-specific variants) to isolate their specific effects on enhancer activity.

2019-11-26 | GSE140983 | GEO

DNA-seq of the QSi5 and 129T2/SvEms mouse strains

Project description:For this project, we explored the genetic determinants of the heart development condition termed patent foramen ovale (PFO) using quantitative trait loci (QTL) mapping and genomics/transcriptomics analyses. Two mice strains were chosen that exhibit highly divergent phenotypes associated with PFO, 129T2/SvEms and QSi5. In this experiment, we performed whole genome sequencing (WGS) on genomic DNA extracted from liver specimens of 129T2/SvEms or QSi5 mice in order to identify genomic variants that may contribute to the phenotypes associated with PFO.

2023-03-31 | E-MTAB-11161 | biostudies-arrayexpress

Project description:Escherichia coli LngA Variants and phenotypes

| PRJNA774369 | ENA

Profiling of chromatin accessibility across multiple tissues and developmental stages of pig [ATAC-seq]

Project description:Landscape of chromatin accessibility across tissues and developmental stages is essential to elucidate the transcriptional regulation in various biological processes and phenotypes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development have been seldomly investigated. Here, we profiled open chromatin maps and transcriptional features of the heart, kidney, liver, lung, skeletal muscle, and spleen tissues in newborn pigs and that of porcine liver tissue at suckling and adult stages using ATAC-seq and rRNA-depleted RNA-seq, respectively. Employing a union set of protein coding genes (PCGs) and two kinds of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue or developmental stage. The PCGs with tissue-specific accessible promoters, as expected, had active transcription and were relevant to tissue-specific functions. Other non-coding tissue-specific peaks were involved in both physical activities and morphogenesis in the neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands the understanding of epigenetic regulation in mammalian tissue functions and organ development, which can benefit both economic trait improvement and better biomedical use of pigs.

2023-08-15 | GSE229520 | GEO

Profiling of chromatin accessibility across multiple tissues and developmental stages of pig [RNA-seq]

2023-08-15 | GSE229521 | GEO

Project description:Virus variants within ASFV infected pigs

| PRJNA1065849 | ENA

Time-resolved phosphotyrosine-proteome of Src signaling

Project description:Intracellular signaling nodes can sample multiple inputs and induce different cellular outputs. High combinatorial between their numerous potential conformational intermediaries having distinct enzymatic activities and/or repertoire of partners makes it challenging to determine their dynamic coding molecularly. We have combined protein engineering with optogenetic to investigate coding functions of specific intermediaries of the kinase Src, a representative example of versatile signaling node. Optogenetic is used to generate local flux of specific Src intermediaries, as Src dimers, into adhesion sites. Modulations of this molecular flux are sufficient to code different Src signaling pathways and Src-dependent cellular outputs implicated in migration or invasion. This response selectivity is based on the ability for each flux of Src conformational intermediary to generate distinct Src signaling waves in protein-protein interaction networks revealed by time-resolved analysis of phosphotyrosine-proteome. Thus, the pleiotropy of a signaling node is molecularly coded by modulation of its local fluxes of specific conformational intermediaries.

2021-02-03 | PXD008534 | Pride

Sus scrofa

Project description:1k pigs project

| PRJNA754250 | ENA