cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26348218
title: Comprehensive cognition of yak (<i>Bos grunniens</i>) <i>AIFM2</i> gene and its anti-ferroptosis role in bisphenol A-induced fetal fibroblast model

description: Apoptosis-inducing factor mitochondrion-associated 2 (<i>AIFM2</i>) has been identified as a gene with anti-ferroptosis properties. To explore whether <i>AIFM2</i> exerts anti-ferroptosis role in yaks (<i>Bos grunniens</i>), we cloned yak <i>AIFM2</i> gene and analyzed its biological characteristics. The coding region of <i>AIFM2</i> had 1122 bp and encoded 373 amino acids, which was conserved in mammals. Next, RT-qPCR results showed an extensive expression of <i>AIMF2</i> in yak tissues. Furthermore, we isolated yak skin fibroblasts (YSFs) and established a bisphenol A (BPA)-induced ferroptosis model to further investigate the role of <i>AIFM2</i>. BPA elevated oxidative stress (reactive oxygen species, ROS) and lipid peroxidation (malondialdehyde, MDA and BODIPY), and reduced cell viability and antioxidant capacity (glutathione, GSH), with the severity depending on the dosage. Of note, a supplement of Ferrostatin-1 (Fer), an inhibitor of ferroptosis, restored the previously mentioned indicators. Subsequently, we constructed an <i>AIFM2</i> overexpression vector and designed <i>AIFM2</i> specific interfering siRNAs, which were transfected into YSFs. The results showed that overexpressing <i>AIFM2</i> alleviated ferroptosis, characterizing by significant changes of cell viability, ROS, BODIPY, MDA and GSH. Meanwhile, interfering <i>AIFM2</i> aggravated ferroptosis, demonstrating the critical anti-ferroptosis role of the yak <i>AIFM2</i> gene. This study shed light on further exploring the molecular mechanism of <i>AIFM2</i> in plateau adaptability.
DOI: 10.6084/m9.figshare.26348218.v1
title: Comprehensive cognition of yak (<i>Bos grunniens</i>) <i>AIFM2</i> gene and its anti-ferroptosis role in bisphenol A-induced fetal fibroblast model

description: Apoptosis-inducing factor mitochondrion-associated 2 (<i>AIFM2</i>) has been identified as a gene with anti-ferroptosis properties. To explore whether <i>AIFM2</i> exerts anti-ferroptosis role in yaks (<i>Bos grunniens</i>), we cloned yak <i>AIFM2</i> gene and analyzed its biological characteristics. The coding region of <i>AIFM2</i> had 1122 bp and encoded 373 amino acids, which was conserved in mammals. Next, RT-qPCR results showed an extensive expression of <i>AIMF2</i> in yak tissues. Furthermore, we isolated yak skin fibroblasts (YSFs) and established a bisphenol A (BPA)-induced ferroptosis model to further investigate the role of <i>AIFM2</i>. BPA elevated oxidative stress (reactive oxygen species, ROS) and lipid peroxidation (malondialdehyde, MDA and BODIPY), and reduced cell viability and antioxidant capacity (glutathione, GSH), with the severity depending on the dosage. Of note, a supplement of Ferrostatin-1 (Fer), an inhibitor of ferroptosis, restored the previously mentioned indicators. Subsequently, we constructed an <i>AIFM2</i> overexpression vector and designed <i>AIFM2</i> specific interfering siRNAs, which were transfected into YSFs. The results showed that overexpressing <i>AIFM2</i> alleviated ferroptosis, characterizing by significant changes of cell viability, ROS, BODIPY, MDA and GSH. Meanwhile, interfering <i>AIFM2</i> aggravated ferroptosis, demonstrating the critical anti-ferroptosis role of the yak <i>AIFM2</i> gene. This study shed light on further exploring the molecular mechanism of <i>AIFM2</i> in plateau adaptability.
DOI: 10.6084/m9.figshare.24905403
title: RNA-seq analysis of small intestine transcriptional changes induced by starvation stress in piglets

description: Piglets may experience a variety of stress injuries, but the molecular regulatory mechanisms underlying these injuries are not well understood. In this study, we analysed the ileum of Large White (LW) and Mashen (MS) piglets at different times of starvation using chemical staining and transcriptome analysis. The intestinal barrier of piglets was damaged after starvation stress, but the intestinal antistress ability of MS piglets was stronger than LW piglets. A total of 8021 differentially expressed genes (DEGs) were identified in two breeds. Interestingly, the immune capacity (<i>CHUK</i>, <i>TLR3</i>) of MS piglets increased significantly after short-term starvation stress, while energy metabolism (<i>NAGS</i>, <i>PLA2G12B</i>, <i>AGCG8</i>) was predominant in LW piglets. After long-term starvation stress, the level of energy metabolism (<i>PLIN5</i>, <i>PLA2G12B</i>) was significantly increased in MS piglets. The expression of immune (<i>HLA-DQB1</i>, <i>IGHG4</i>, <i>COL3A1</i>, <i>CD28</i>, <i>LAT</i>) and disease (<i>HSPA1B</i>, <i>MINPPI</i>, <i>ADH1C</i>, <i>GAL3ST1</i>) related genes were significantly increased in two breeds of piglets. These results suggest that short-term stress mainly enhances immunity and energy metabolism in piglets, while long-term starvation produces greater stress on piglets, making it difficult for them to compensate for the damage to their bodies through self-regulation. This information can help improve the stress resistance of piglets through molecular breeding.
DOI: 10.6084/m9.figshare.24905403.v1
title: RNA-seq analysis of small intestine transcriptional changes induced by starvation stress in piglets

description: Piglets may experience a variety of stress injuries, but the molecular regulatory mechanisms underlying these injuries are not well understood. In this study, we analysed the ileum of Large White (LW) and Mashen (MS) piglets at different times of starvation using chemical staining and transcriptome analysis. The intestinal barrier of piglets was damaged after starvation stress, but the intestinal antistress ability of MS piglets was stronger than LW piglets. A total of 8021 differentially expressed genes (DEGs) were identified in two breeds. Interestingly, the immune capacity (<i>CHUK</i>, <i>TLR3</i>) of MS piglets increased significantly after short-term starvation stress, while energy metabolism (<i>NAGS</i>, <i>PLA2G12B</i>, <i>AGCG8</i>) was predominant in LW piglets. After long-term starvation stress, the level of energy metabolism (<i>PLIN5</i>, <i>PLA2G12B</i>) was significantly increased in MS piglets. The expression of immune (<i>HLA-DQB1</i>, <i>IGHG4</i>, <i>COL3A1</i>, <i>CD28</i>, <i>LAT</i>) and disease (<i>HSPA1B</i>, <i>MINPPI</i>, <i>ADH1C</i>, <i>GAL3ST1</i>) related genes were significantly increased in two breeds of piglets. These results suggest that short-term stress mainly enhances immunity and energy metabolism in piglets, while long-term starvation produces greater stress on piglets, making it difficult for them to compensate for the damage to their bodies through self-regulation. This information can help improve the stress resistance of piglets through molecular breeding.
DOI: 10.6084/m9.figshare.24968765
title: Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (<i>Bos grunniens</i>)

description: The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.
DOI: 10.6084/m9.figshare.24968765.v1
title: Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (<i>Bos grunniens</i>)

description: The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.
DOI: 10.6084/m9.figshare.25464644
title: Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum

description: Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host–microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including <i>Bacteroides</i> and <i>Peptostreptococcacea</i>. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (<i>ACADL</i>), Acyl-CoA Oxidase (<i>ACOX</i>) and Acetyl-CoA Acyltransferase (<i>ACAA</i>). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.
DOI: 10.6084/m9.figshare.25464644.v1
title: Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum

description: Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host–microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including <i>Bacteroides</i> and <i>Peptostreptococcacea</i>. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (<i>ACADL</i>), Acyl-CoA Oxidase (<i>ACOX</i>) and Acetyl-CoA Acyltransferase (<i>ACAA</i>). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.
DOI: 10.6084/m9.figshare.25610700
title: MiR-2284b regulation of α-s1 casein synthesis in mammary epithelial cells of dairy goats

description: The lactation character of dairy goats is the most important characteristic, and milk protein is an important index to evaluate milk quality. Casein accounts for more than 80% of the total milk protein in goat milk and is the main component of milk protein. Using GMECs (goat mammary epithelial cells) as the research object, the CHECK2 vector of the CSN1S1 gene and the overexpression vector of pcDNA 3.1 were constructed, and the mimics of miR-2284b and the interfering RNA of CSN1S1 were synthesized. Using PCR, RT–qPCR, a dual luciferase activity detection system, EdU, CCK8, cell apoptosis detection and ELISA detection, we explored the regulatory mechanism and molecular mechanism of miR-2284b regulation of αs1-casein synthesis in GMECs. miR-2284b negatively regulates proliferation and apoptosis of GMECs and αs1-casein synthesis. Two new gene sequences of CSN1S1 were discovered. CSN1S1-1/-2 promoted the proliferation of GMECs and inhibited cell apoptosis. However, it had no effect on αs1-casein synthesis. MiR-2284b negatively regulates αs1-casein synthesis in GMECs by inhibiting the CSN1S1 gene. These results all indicated that miR-2284b could regulate αs1-casein synthesis, thus playing a theoretical guiding role in the future breeding process of dairy goats and accelerating the development of dairy goat breeding.
DOI: 10.6084/m9.figshare.25610700.v1
title: MiR-2284b regulation of α-s1 casein synthesis in mammary epithelial cells of dairy goats

description: The lactation character of dairy goats is the most important characteristic, and milk protein is an important index to evaluate milk quality. Casein accounts for more than 80% of the total milk protein in goat milk and is the main component of milk protein. Using GMECs (goat mammary epithelial cells) as the research object, the CHECK2 vector of the CSN1S1 gene and the overexpression vector of pcDNA 3.1 were constructed, and the mimics of miR-2284b and the interfering RNA of CSN1S1 were synthesized. Using PCR, RT–qPCR, a dual luciferase activity detection system, EdU, CCK8, cell apoptosis detection and ELISA detection, we explored the regulatory mechanism and molecular mechanism of miR-2284b regulation of αs1-casein synthesis in GMECs. miR-2284b negatively regulates proliferation and apoptosis of GMECs and αs1-casein synthesis. Two new gene sequences of CSN1S1 were discovered. CSN1S1-1/-2 promoted the proliferation of GMECs and inhibited cell apoptosis. However, it had no effect on αs1-casein synthesis. MiR-2284b negatively regulates αs1-casein synthesis in GMECs by inhibiting the CSN1S1 gene. These results all indicated that miR-2284b could regulate αs1-casein synthesis, thus playing a theoretical guiding role in the future breeding process of dairy goats and accelerating the development of dairy goat breeding.
DOI: 10.6084/m9.figshare.24899769
title: Transcriptome sequencing analysis of bovine mammary epithelial cells induced by lipopolysaccharide

description: Mastitis in cows is caused by the inflammation of the mammary glands due to an infection by external pathogenic bacteria. Mammary gland epithelial cells, which are in direct contact with the external environment, are responsible for the first line of defense of the mammary gland against pathogenic bacteria, playing an essential role in immune defense. To investigate the mechanism of bovine mammary epithelial cells in the inflammatory process, we treated the cells with LPS for 12 hours and analyzed the changes in mRNA by transcriptome sequencing. The results showed that compared to the control group, the LPS treatment group had 121 up-regulated genes and 18 down-regulated genes. GO and KEGG enrichment analysis revealed that these differential genes were mainly enriched in the IL-17 signaling pathway, Legionellosis, Cytokine-cytokine receptor interaction, NF-kappa B signaling pathway, and other signaling pathways. Furthermore, the expression of GRO1 and CXCL3 mRNAs increased significantly after LPS treatment. These findings provide new insights for the treatment of mastitis in cows in the future.
DOI: 10.6084/m9.figshare.24899769.v1
title: Transcriptome sequencing analysis of bovine mammary epithelial cells induced by lipopolysaccharide

description: Mastitis in cows is caused by the inflammation of the mammary glands due to an infection by external pathogenic bacteria. Mammary gland epithelial cells, which are in direct contact with the external environment, are responsible for the first line of defense of the mammary gland against pathogenic bacteria, playing an essential role in immune defense. To investigate the mechanism of bovine mammary epithelial cells in the inflammatory process, we treated the cells with LPS for 12 hours and analyzed the changes in mRNA by transcriptome sequencing. The results showed that compared to the control group, the LPS treatment group had 121 up-regulated genes and 18 down-regulated genes. GO and KEGG enrichment analysis revealed that these differential genes were mainly enriched in the IL-17 signaling pathway, Legionellosis, Cytokine-cytokine receptor interaction, NF-kappa B signaling pathway, and other signaling pathways. Furthermore, the expression of GRO1 and CXCL3 mRNAs increased significantly after LPS treatment. These findings provide new insights for the treatment of mastitis in cows in the future.
DOI: 10.5281/zenodo.17921082
title: Svalbox-DOM_2025-0005

description: Model description: Digital outcrop model Sverrefjellet, Haakon VII Land, Svalbard archipelago. Volcanic dikes.Data availability:All uploaded archives are to be extracted to the same directory for a functional working environment, i.e., at the very least consisting of a project folder with the data and metashape subdirectories. The included processing report specifies the processing parameters that were used as input for the processing software (Agisoft Metashape, v2.2.1.20641).Exported model data use CRS epsg:32633.Show and visualise on Svalbox.no:Through Svalbox we aim to take geoscientific research and education to the next level – with the simple motto of placing all key information and data sets in their correct spatial position. We bring modern technology, in particular cost-effective digital outcrops, to complement more than 200 years of geoscientific research on Svalbard. Finally, Svalbox provides a sustainable platform for sharing results, workflows and teaching material with the wider geoscientific community.For more information, contact the Svalbox team at svalbox[at]gmail.com.This data set forms part of the Svalbox Digital Model Database.Please cite the database alongside this resource:Betlem, Peter and Rodes, Nil and Birchall, Thomas and Dahlin, Anders and Smyrak-Sikora, Aleksandra and Senger, Kim. The Svalbox Digital Model Database: A Geoscientific Window into the High Arctic. Geosphere (2023) 19 (6): 1640-1666. https://doi.org/10.1130/GES02606.1
DOI: 10.5281/zenodo.17921083
title: Svalbox-DOM_2025-0005

description: Model description: Digital outcrop model Sverrefjellet, Haakon VII Land, Svalbard archipelago. Volcanic dikes.Data availability:All uploaded archives are to be extracted to the same directory for a functional working environment, i.e., at the very least consisting of a project folder with the data and metashape subdirectories. The included processing report specifies the processing parameters that were used as input for the processing software (Agisoft Metashape, v2.2.1.20641).Exported model data use CRS epsg:32633.Show and visualise on Svalbox.no:Through Svalbox we aim to take geoscientific research and education to the next level – with the simple motto of placing all key information and data sets in their correct spatial position. We bring modern technology, in particular cost-effective digital outcrops, to complement more than 200 years of geoscientific research on Svalbard. Finally, Svalbox provides a sustainable platform for sharing results, workflows and teaching material with the wider geoscientific community.For more information, contact the Svalbox team at svalbox[at]gmail.com.This data set forms part of the Svalbox Digital Model Database.Please cite the database alongside this resource:Betlem, Peter and Rodes, Nil and Birchall, Thomas and Dahlin, Anders and Smyrak-Sikora, Aleksandra and Senger, Kim. The Svalbox Digital Model Database: A Geoscientific Window into the High Arctic. Geosphere (2023) 19 (6): 1640-1666. https://doi.org/10.1130/GES02606.1
DOI: 10.6084/m9.figshare.26371456
title: Molecular signatures diversity unveiled through a comparative transcriptome analysis of longissimus dorsi and psoas major muscles in Hanwoo cattle

description: This study investigates the transcriptome-level alterations that influence production traits and early fattening stage myogenesis in Hanwoo cattle, specifically focusing on the highly prized Longissimus dorsi (LD) and Psoas major (PM) skeletal muscles, which hold significant commercial value. We conducted RNA sequencing analysis on LD and PM muscles from 14 Hanwoo steers (<i>n</i> = 7, each group) at the age of 10 months, all fed the same diet. Our results unveiled a total of 374 and 206 up-regulated differentially expressed genes (DEGs) in LD and PM muscles, respectively, with statistical significance (<i>p</i> &lt; 0.05) and a log<sub>2</sub>fold change ≥ 1. Genes governing muscle development processes, such as <i>PAX3</i>, <i>MYL3</i>, <i>COL11A1</i>, and <i>MYL6B</i>, were found to be expressed at higher levels in both tissues. Conversely, genes regulating lipid metabolism, including <i>FABP3</i>, <i>FABP4</i>, <i>LEP</i>, <i>ADIPOQ</i>, and <i>PLIN1</i>, exhibited higher expression in the PM muscle. Functional enrichment analysis revealed a tissue-specific response, as PM muscle showed increased lipid metabolism allied pathways, including the PPAR signaling pathway and regulation of lipolysis in adipocytes, while LD was characterized by growth and proliferative processes. Our findings validate the presence of a muscle-dependent transcription and co-expression pattern that elucidates the transcriptional landscape of bovine skeletal muscle.