Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8631870_1.fastq.gz | Fastqsanger.gz | |||
| SRR8631870_2.fastq.gz | Fastqsanger.gz | |||
| SRR8631871_1.fastq.gz | Fastqsanger.gz | |||
| SRR8631871_2.fastq.gz | Fastqsanger.gz | |||
| SRR8631866_1.fastq.gz | Fastqsanger.gz |
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Project description:To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels. Liver mRNA profiles of intact male pigs fed a HFC diet, castrated male pigs fed a HFC diet, and castrated male pigs treated with testosterone fed a HFC diet were generated by deep sequencing, using Illumina HiSeq 2000.
2015-01-08 | E-GEOD-62696 | biostudies-arrayexpress
Project description:To gain insight into the role of testosterone in modulating hepatic fat accumulation, we collected liver tissues from high fat diet-fed intact male pigs, castrated male pigs, and castrated male pigs with testosterone replacement. RNA-Seq was employed to profile hepatic gene expression in pigs with different testosterone levels.
2015-01-08 | GSE62696 | GEO
Project description:Liver development and metabolic adaptation are well-orchestrated by a series of signaling pathways and genes. Chromatin architecture is known to influence gene expression, yet its role in controlling liver development and metabolism remains unclear. We performed high-throughput chromatin conformation capture sequencing (HiC-seq) and integrated RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) on liver tissue that were collected from six key developmental stages (embryonic day 38 [E38] – 2 years [2y]) and a high fat diet (HFD) feeding group. Our data revealed global three-dimensional (3D) reorganization during liver development from the scales of compartment, topologically associated domain (TAD) and promoter-enhancer interaction (PEI), which consistently affects the expression level of genes known to be important for liver development and function. Comparison of 3D genome and gene expression profiles between pig liver development and human hepatocellular carcinoma (HCC) revealed similarities between fatal liver and HCC and provided potential explanation for the aberrant expression in HCC from the perspective of chromatin architecture. Moreover, the similar genome architecture and expression of genes related to lipid metabolism between nomally and HFD feeding pigs, along with the thicker back fat in HFD feeding pigs compared to normally feeding pigs, supported that pigs are resistant to nonalcoholic fatty liver disease (NAFLD). Together, our results provide a global view of dynamic chromatin interactions during liver development and metabolic adaptation induced by HFD feeding, which may open new avenues for liver research and HCC therapeutic interventions.
2022-03-15 | GSE176387 | GEO
Project description:This dataset includes 2*76bp RNA-seq reads from 9 pigs sequenced using Illumina NextSeq500.
| EGAD00001009783 | EGA
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
Project description:Co-expression network analysis using DNA oligonucleotide microarrays of experimentally infected pigs. The expression profiles of liver from ten experimentally infected pigs were compared with the profiles of liver from five non-infected contol pigs. The expression profiles of liver from ten experimentally infected pigs were compared with the profiles of liver from five non-infected contol pigs.
2013-01-01 | E-GEOD-25181 | biostudies-arrayexpress
Project description:Co-expression network analysis using DNA oligonucleotide microarrays of experimentally infected pigs. The expression profiles of liver from ten experimentally infected pigs were compared with the profiles of liver from five non-infected contol pigs.
2013-01-01 | GSE25181 | GEO
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 | GSE229521 | GEO
Project description:Based on the work flow of quantitative proteomic analysis combined with TMT labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS), this study carried out quantitative proteomic analysis on the liver tissues of Tibetan pigs and Yorkshire pigs in Shannan (about 4000 m), Linzhi (about 3000 m) and Jiuzhaigou (about 1500 m), and compared the differences of protein mass spectra between the liver of living pigs at three altitudes.
2023-03-11 | PXD039758 | Pride