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Series GSE162145 Query DataSets for GSE162145
Status Public on Apr 20, 2021
Title A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [RNA-Seq pig]
Organism Sus scrofa
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Comprehensive transcriptomic survey of the pig (Sus scrofa) may lead to a better understanding of mechanisms of tissue specialization that underlie economic traits of this species and accelerate its use as a biomedical model. Here, we characterized four distinct transcript types (lncRNAs, TUCPs, miRNAs and circRNAs) in 31 adult pig tissues and two cell lines, together with protein-coding genes. We dissected their distinct structural and transcriptional features and uncovered transcriptome variability as related to tissue physiology. We discovered extraordinary diversity among 47 anatomically distinct skeletal muscle types, as well as among six adipose depots, which are linked to their diverse origins, metabolic features, cell composition, physical activity and mitochondrial pathways. In particular, transcription of HOX genes across skeletal muscles exhibited a position-dominant pattern, revealing a similar developmental history of these tissues within the same body part. Transcriptional patterns across adipose depots demonstrated a metabolically protective role of subcutaneous adipose tissue and the association of visceral adipose tissue with metabolic dysfunction. Comparative analysis of the transcriptomes of seven tissues of the pig and nine other vertebrates revealed insights into evolutionary divergence of transcription that contributes to lineage-specific tissue biology. We also analyzed long-range regulation of promoters by their enhancers with downstream transcription in subcutaneous adipose tissues of six mammals, showing that evolutionary stability of transcription can mainly be attributed to multiple enhancers buffering gene expression patterns against genetic perturbations, thereby conferring robustness during speciation. Collectively, this study offers a resource for the accelerated use of the pig as a biomedical model for human biology and disease and uncovers molecular bases of its diverse economic traits.
 
Overall design We generated RNA sequencing (RNA-seq) data of pig tissues of 1-3 replicates.
 
Contributor(s) Jin L, Hu S, Li M, Tang Q
Citation(s) 34140474
BioProject PRJNA637678
Submission date Nov 25, 2020
Last update date Mar 23, 2022
Contact name jin long
E-mail(s) longjin8806@163.com
Organization name Sichuan Agricultural University
Street address Hui ming
City Chengdu
ZIP/Postal code 611130
Country China
 
Platforms (1)
GPL22918 HiSeq X Ten (Sus scrofa)
Samples (194)
GSM4943008 RNA sequencing ADD-1 biological replicate 1
GSM4943009 RNA sequencing ADD-2 biological replicate 2
GSM4943010 RNA sequencing ADD-3 biological replicate 3
This SubSeries is part of SuperSeries:
GSE162148 A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription
Relations
SRA SRP266207

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE162145_analysis.gtf.gz 17.4 Mb (ftp)(http) GTF
GSE162145_pig_PCG.all_exp_tpm_gene.txt.gz 7.5 Mb (ftp)(http) TXT
GSE162145_pig_TUCP.all_exp_tpm_gene.txt.gz 674.1 Kb (ftp)(http) TXT
GSE162145_pig_circRNA.all_exp_tpm_gene.txt.gz 4.2 Mb (ftp)(http) TXT
GSE162145_pig_lncRNA.all_exp_tpm_gene.txt.gz 5.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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