Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1162664 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30717974_1.fastq.gz | Fastqsanger.gz | |||
| SRR30717974_2.fastq.gz | Fastqsanger.gz | |||
| SRR30717975_1.fastq.gz | Fastqsanger.gz | |||
| SRR30717975_2.fastq.gz | Fastqsanger.gz | |||
| SRR30717976_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: High-altitude adaptive evolution of transcription, and the convergence and divergence of transcriptional alteration across species in response to high-altitude environments, is an important topic of broad interest to the general biology community. Our study aims to answer this important biological question. Methods: We generated deep transcriptome data of high- and low- altitude populations across four species: chicken, pig, goat and sheep, as well as high-altitude yak and low-altitude cattle, from six tissues (heart, kidney, liver, lung, skeletal muscle and spleen). Results: Here we provide a comprehensive comparative transcriptome landscape of expression and alternative splicing variation between low- and high-altitude populations across multiple species for distinct tissues. Conclusions: Our data serves a valuable resource for further study on adaptive transcription evolution and identification of candidate adaptive genes.
2017-09-06 | GSE93855 | GEO
Project description:This study explores how yaks, an ideal animal model for studying plateau adaptability, adapt to high-altitude environments. The lung is a representative organ of the yak’s adaptation to high-altitude environments. The F1 hybrids of yak and cattle, known as dzho, also exhibit adaptability to plateau conditions. This study constructed a single-cell transcriptome atlas of the lungs in yak, dzho and cattle, containing 51 subtypes. We initially found that the differential subtypes among yak, dzho and cattle were mainly concentrated in T&NK cells and fibroblasts. Most of them belonged to new cell subtypes. Subsequently, we speculated that NKG7 and CD4 played a central regulatory role in T&NK cells, contributing to T cell activation and affecting the adaptive immune response of yaks. In fibroblasts, MYL9 and IGF2 are believed to play key regulatory roles, participating in maintaining cellular energy metabolism balance. These results provide an important scientific basis for systematically analysing the molecular regulatory mechanisms of yak adaptation to high-altitude hypoxia.
2024-05-03 | GSE266061 | GEO
Project description:Purpose: The goal of this study was to compare the microRNA transcriptomes of four high-altitude vertebrates and their low-altitude relatives for six organs (heart,liver,spleen,lung,kidney and muscle). Methods: Three adult females for each population of the five species from distinct altitudes (600 m, 2000 m, and 3000 m) were humanely killed to ameliorate suffering. A piece of tissue fragments from six organs including heart, liver, spleen, lung, kidney and skeletal muscle(longissimus muscle for pig, cattle, yak and sheep, and pectoral muscle for chicken) were used to extract total RNA. Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit and sequenced on the Illumina HiSeq 2500. The raw data were submitted to miRDeep2.0 to detect miRNAs for each species with default parameters. Results: we detected 2,036 mature miRNAs in five species and identified 49 orthologues among vertebrate, 111 orthologues in artiodactyla and 171 orthologues in ruminant . Conclusions: We identified comparable numbers of miRNAs in each species.
2019-08-19 | GSE124418 | GEO
Project description:Purpose：Yak long-term colonization and widespread distribution across the plateau can be serve as an ideal natural animal model to provide insights into the adaptive evolution of other plateau species, including humans. Methods:To exploring the molecular mechanisms of lung tissue in yak to response to hypoxia, the mRNA, lncRNA and miRNA of lung tissue from cattle and three different altitude yaks were sequenced. Results:A total of 21764 mRNAs, 14168 lncRNAs and 1209miRNAs (305 known and 904 novel miRNAs)were identifed.Compared yak with cattle, 4975 mRNAs, 3326 lncRNAs and 75 miRNAs were differentially expressed. 756 mRNAs, 346 lncRNAs and 83 miRNAs were found to be differentially expressed amongthree different altitude yaks(fold change≥2 and P-value<0.05). Conclusions:The differentially expressed genes were functionally enriched in long-chain fatty acid metabolic process and protein processing between yak and cattle, while the immune response and cell cycle were enriched among three different altitude yaks. Furthermore, the competing endogenous RNAs (ceRNAs) networks were identified to illustrate their roles.
2020-07-08 | GSE153962 | GEO
Project description:Purpose：Yak long-term colonization and widespread distribution across the plateau can be serve as an ideal natural animal model to provide insights into the adaptive evolution of other plateau species, including humans. Methods:To exploring the molecular mechanisms of lung tissue in yak to response to hypoxia, the mRNA, lncRNA and miRNA of lung tissue from cattle and three different altitude yaks were sequenced. Results:A total of 21764 mRNAs, 14168 lncRNAs and 1209miRNAs (305 known and 904 novel miRNAs)were identifed.Compared yak with cattle, 4975 mRNAs, 3326 lncRNAs and 75 miRNAs were differentially expressed. 756 mRNAs, 346 lncRNAs and 83 miRNAs were found to be differentially expressed amongthree different altitude yaks(fold change≥2 and P-value<0.05). Conclusions:The differentially expressed genes were functionally enriched in long-chain fatty acid metabolic process and protein processing between yak and cattle, while the immune response and cell cycle were enriched among three different altitude yaks. Furthermore, the competing endogenous RNAs (ceRNAs) networks were identified to illustrate their roles.
2020-07-08 | GSE153956 | GEO
Project description:Purpose: The goal of this study was to reveal epigenetic differences in the microRNA transcriptomes of two organs (heart and lung) between yak and cattle. Methods: Three unrelated 2-year old adult females for both of yaks and cattle (Luxi Huang cattle) were used in this study. Two of significant hypoxia-responsive tissues (heart and lung) were rapidly collected from each carcass, washed three times with physiological saline, immediately frozen in liquid nitrogen. All frozen samples were stored at –80 °C until RNA extraction.The total RNA were extracted with Trizol (Ambion, USA). NanoDrop ND-2000 spectrophotometer (Nano Drop, DE, USA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) were used to monitor the concentration and integrity of RNA, respectively. In brief, several successive steps consist the Illumina sequencing. The small RNA with length of 14-40 nt were first purified by polyacrylamide gel electrophoresis (PAGE), and then specific adapters were ligated to the purified small RNA. The ligated RNA were reverse transcribed to cDNA libraries. Finally, each library were sequenced on Genome Analyzer. Results: We identified 808 widely-expressed conserved and 697 species-specific novel miRNAs in two species. In addition, although two organs showed similar high expression miRNAs, larger differentiation was present in lung than heart between two species. In addition, miRNAs with significantly differentiated patterns of expression in two organs exhibited obvious co-operation effect in high altitude adaptation in form of miRNA family and cluster. Functional analysis revealed that a large amount of differentially expressed miRNAs were enriched in hypoxia-related pathways, such as VEGF signaling pathway, HIF-1α signaling pathway, insulin signaling pathway, DNA damage response, apoptosis, fatty acid metabolism and glucose metabolism. These results suggested the diverse degrees of epigenetic variation in different tissues between yak and cattle, and revealed extensive roles of miRNAs in high altitude adaptation. Conclusions: In this study, we illustrated the differences in the microRNA transcriptomes level for heart and lung between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation. The work performed here will provide a typical demonstration for future deciphering the mechanism of high altitude adaptation
2017-03-31 | GSE87833 | GEO
Project description:Cattle-yak is the hybrid offspring of yak and cattle. It has obvious heterosis in production performance, but the male sterility of cattle-yak has always been the focus of attention. Studies have shown that non-coding RNA is involved in the regulation of spermatogenesis. We comprehensively compared the testicular transcription profiles of cattle, yak and cattle-yak. More DEGs, DECs and DEMs were found in the intersection of the two comparison groups of cattle and cattle-yak, yak and cattle-yak, with 4,968, 360 and 59, respectively. The DEGs of cattle-yak, cattle and yak were mainly enriched in biological processes such as spermatogenesis, male gamete generation and sexual reproduction. At the same time, GO and KEGG analysis suggested that DECs host genes and DEMs source genes were also involved in the regulation of spermatogenesis. The construction of potential ceRNA networks found that some differentially expressed ncRNAs may be involved in the regulation of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, miR-15b, etc., as well as unreported miR-6123, miR-1306 and some miRNA and circRNA interaction pairs. This study provides a reference for further study on the mechanism of male sterility in cattle-yak.
2024-02-06 | GSE254886 | GEO
Project description:The transcriptome signature of peripheral blood mononuclear cells (PBMCs) of Ladakhi cattle adapted to high altitude vis a vis Sahiwal cattle adapted to the arid/semi-arid region at mean sea level was established using bovine expression microarray chips. The transcriptome analysis of PBMCs from these cattle types living at two distinct altitudes, resulted in identification of several hundred differentially expressed genes, biological processes, molecular functions and pathways.
2021-07-09 | GSE116800 | GEO
Project description:This study used yak and cattle-yak testes from different developmental stages as materials to construct a complete translation map of the testes, and integrated transcriptome and translation results to explore gene expression changes during the sexual maturation process of yak testes. This study utilized Ribo seq technology to construct a transcriptome map of yak testicular development, revealing that the expression of genes related to spermatogenesis is specifically translated and regulated at different developmental stages. In addition, many unknown open reading frames (ORFs) in the testes have been newly identified.
2024-08-30 | GSE270057 | GEO
Project description:High altitude exposes humans to hypobaric and hypoxic conditions, which induce various physiological and molecular changes. Recent evidence, mostly from animal models, points towards interaction between circadian rhythms and the hypoxic response, however their human relevance is largely unknown. To examine the interaction between elevated altitude-low oxygen and daily rhythms, we analyzed the effect of different high altitudes in conjunction with day-time on human whole blood transcriptome. We found that high altitude vastly affects the blood transcriptome and unexpectedly, does not necessarily follow a monotonic response to altitude elevation. We observed daily variance in gene expression, which was largely dependent on altitude. Moreover, using digital cytometry approach we estimated the relative changes in abundance of different cell types and found the several immune cell types were responding in a time- and altitude-dependent manner. Taken together, our data shed new light on the transcriptional response to high altitude and its interaction with daily rhythms.
2022-03-03 | GSE196728 | GEO