cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23654402.v2
title: Two novel SNPs identified in <i>STAT1</i> gene adjoining a QTL for milk production in Holstein Friesian crossbreds of Kerala

description: We analyzed the effect of a single nucleotide polymorphism, g. C3141T in the 3′ UTR of Signal transducer and activator of transcription-1 gene (<i>STAT1</i>) on milk production traits in the Holstein Friesian crossbred cattle of Kerala (n = 144) by association analysis and expression study. The population was genotyped by restriction fragment length polymorphism using <i>Pag</i>1. Association study using the General Linear Model-Analysis of Variance revealed that none of the yield or composition traits analyzed were significantly differed. The expression profile of <i>STAT1</i> gene in leucocytes of animals bearing homozygous genotypes was compared by quantitative real time PCR using SYBR green chemistry with and relative expression was not found to be significantly differed. The second stage of the study, the <i>STAT1</i> mRNA spanning 3213 bp was amplified from leucocytes and sequenced (GenBank: MT459802.1). Two novel SNPs were identified; one synonymous mutation in the coding region (g.A1212G) and the other in the 3'UTR (g.T3042C). The novel SNPs might contribute to <i>STAT1</i> gene regulation mediated by alternate spicing or binding sites for regulatory molecules. The results reiterate the importance of extensive studies of <i>STAT1</i> gene variants to substantiate the presence of a quantitative trait loci for dairy traits in the vicinity of <i>STAT1</i> gene.
DOI: 10.6084/m9.figshare.25458853
title: RefEx2 Datasets for Drosophila melanogaster transcriptome

description: RefEx2 is a project to collect, organize, and curate transcriptome datasets of various species as reference resources for gene expression data analysis. It provides 6 reference datasets for four different species: humans, mice, Drosophila melanogaster, and Arabidopsis thaliana. This directory contains the following datasets on Drosophila melanogaster transcriptome: droso2017_refextable_sample_stats.tsv.gzProcessed data matrixdroso2017_refextable_grouped_sample_desc.tsvGrouped sample descriptiondroso2017_refextable_sampleID_mapping.tsvSample ID mappingsNo. of genes: 17,894<br>No. of samples: 32Key ID: NCBI gene<br>Original data: GSE99574<br>Reference(s): DOI: 10.26508/lsa.201800156
DOI: 10.6084/m9.figshare.25458853.v1
title: RefEx2 Datasets for Drosophila melanogaster transcriptome

description: RefEx2 is a project to collect, organize, and curate transcriptome datasets of various species as reference resources for gene expression data analysis. It provides 6 reference datasets for four different species: humans, mice, Drosophila melanogaster, and Arabidopsis thaliana. This directory contains the following datasets on Drosophila melanogaster transcriptome: droso2017_refextable_sample_stats.tsv.gzProcessed data matrixdroso2017_refextable_grouped_sample_desc.tsvGrouped sample descriptiondroso2017_refextable_sampleID_mapping.tsvSample ID mappingsNo. of genes: 17,894<br>No. of samples: 32Key ID: NCBI gene<br>Original data: GSE99574<br>Reference(s): DOI: 10.26508/lsa.201800156
DOI: 10.6084/m9.figshare.24092321
title: Differentially expressed transcripts study during pregnancy and postpartum anestrus of yak (<i>Bos grunniens</i>)

description: <i>Background:</i> Yak is the main livestock species in the plateau area, and its reproductive performance is low, usually two years or three years. A very few of yaks recover within a certain period of time after delivery and smoothly enter the next estrous cycle, while most of them enter the postpartum anestrus and show no estrus performance. However, the key biological factors and influencing mechanisms that cause postpartum anestrus in yaks are not clear. <i>Objective:</i> To study the expression of differential transcripts in ovaries of yak during pregnancy and postpartum anestrus. <i>Methods:</i> Each three yaks in pregnancy and anestrus under natural grazing conditions in Haiyan County, Qinghai Province were selected and slaughtered, and their ovaries were collected and sent to Biomarker Technologies. Oxford Nanopore Technologies single-molecule real-time electrical signal sequencing technology was used to perform full-length transcriptome sequencing. Astalavista software was used to identify the types of alternative splicing events in yak estrus and pregnancy, and TAPIS pipeline was used to identify alternative polyadenylation. <i>Results:</i> The results showed that there were 1751 differentially expressed transcripts (DETs) between pregnancy and anestrus in yak, of which 808 were upregulated and 943 were downregulated. GO analysis showed that the biological processes of DETs were mainly reproductive, reproductive and rhythmic processes. KEGG analysis showed that the DET cell junction-related adhesion junction protein (<i>β-catenin</i>) and amino terminal kinase (<i>JNK</i>) were involved in FAs (local adhesion). Phosphatidylinositol-3-kinase (<i>PI3K</i>) is involved in the PI3K/AKT/mTOR signaling pathway. Circadian rhythm output cycle failure (<i>Clock</i>) and brain and muscle tissue aromatic hydrocarbon receptor nuclear transporter-like protein 1 (<i>Bmal1</i>) are involved in circadian rhythm signaling pathway. <i>Conclusion:</i> This study found that β-catenin, <i>JNK</i>, <i>PI3K</i>, <i>Clock</i> and <i>Bmal1</i> were closely related to postpartum anestrus in yak.
DOI: 10.6084/m9.figshare.24092321.v1
title: Differentially expressed transcripts study during pregnancy and postpartum anestrus of yak (<i>Bos grunniens</i>)

description: <i>Background:</i> Yak is the main livestock species in the plateau area, and its reproductive performance is low, usually two years or three years. A very few of yaks recover within a certain period of time after delivery and smoothly enter the next estrous cycle, while most of them enter the postpartum anestrus and show no estrus performance. However, the key biological factors and influencing mechanisms that cause postpartum anestrus in yaks are not clear. <i>Objective:</i> To study the expression of differential transcripts in ovaries of yak during pregnancy and postpartum anestrus. <i>Methods:</i> Each three yaks in pregnancy and anestrus under natural grazing conditions in Haiyan County, Qinghai Province were selected and slaughtered, and their ovaries were collected and sent to Biomarker Technologies. Oxford Nanopore Technologies single-molecule real-time electrical signal sequencing technology was used to perform full-length transcriptome sequencing. Astalavista software was used to identify the types of alternative splicing events in yak estrus and pregnancy, and TAPIS pipeline was used to identify alternative polyadenylation. <i>Results:</i> The results showed that there were 1751 differentially expressed transcripts (DETs) between pregnancy and anestrus in yak, of which 808 were upregulated and 943 were downregulated. GO analysis showed that the biological processes of DETs were mainly reproductive, reproductive and rhythmic processes. KEGG analysis showed that the DET cell junction-related adhesion junction protein (<i>β-catenin</i>) and amino terminal kinase (<i>JNK</i>) were involved in FAs (local adhesion). Phosphatidylinositol-3-kinase (<i>PI3K</i>) is involved in the PI3K/AKT/mTOR signaling pathway. Circadian rhythm output cycle failure (<i>Clock</i>) and brain and muscle tissue aromatic hydrocarbon receptor nuclear transporter-like protein 1 (<i>Bmal1</i>) are involved in circadian rhythm signaling pathway. <i>Conclusion:</i> This study found that β-catenin, <i>JNK</i>, <i>PI3K</i>, <i>Clock</i> and <i>Bmal1</i> were closely related to postpartum anestrus in yak.
DOI: 10.6084/m9.figshare.23741904
title: Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives – Danubian horse and Serbian Nonius

description: From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses. The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds – the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O’P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O’P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations. In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.
DOI: 10.6084/m9.figshare.23741904.v1
title: Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives – Danubian horse and Serbian Nonius

description: From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses. The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds – the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O’P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O’P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations. In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.
DOI: 10.6084/m9.figshare.23709692
title: Analysis of alternative splicing in chicken macrophages transfected with overexpression/knockdown of <i>RIP2</i> gene

description: Receptor-interacting protein 2 (RIP2) plays a critical role in the transduction of many signaling pathways and is associated with many diseases. Alternative splicing (AS) is an essential and ubiquitous regulatory mechanism of gene expression that contributes to distinct transcript variants and many different kinds of proteins. In this present study, we characterized genome-wide AS events in wild-type chicken macrophages (WT) and <i>RIP2</i> overexpression/knockdown chicken macrophages (oeRIP2/shRIP2) by high-throughput RNA sequencing technology. A total of 1901, 2061, and 817 differentially expressed (DE) AS genes were identified in the comparison of oeRIP2 vs. WT, oeRIP2 vs. shRIP2, and shRIP2 vs. WT, respectively. These DE AS genes participated in many important KEGG pathways, including regulation of autophagy, Wnt signaling pathway, Ubiquitin mediated proteolysis, MAPK signaling pathway, and Focal adhesion, etc. In conclusion, this research provided a broad atlas of the genome-wide scale of the AS event landscape in <i>RIP2</i> overexpression/knockdown and wild-type chicken macrophages. This research also provides the theoretical basis of the gene network related to <i>RIP2</i>.
DOI: 10.6084/m9.figshare.23709692.v1
title: Analysis of alternative splicing in chicken macrophages transfected with overexpression/knockdown of <i>RIP2</i> gene

description: Receptor-interacting protein 2 (RIP2) plays a critical role in the transduction of many signaling pathways and is associated with many diseases. Alternative splicing (AS) is an essential and ubiquitous regulatory mechanism of gene expression that contributes to distinct transcript variants and many different kinds of proteins. In this present study, we characterized genome-wide AS events in wild-type chicken macrophages (WT) and <i>RIP2</i> overexpression/knockdown chicken macrophages (oeRIP2/shRIP2) by high-throughput RNA sequencing technology. A total of 1901, 2061, and 817 differentially expressed (DE) AS genes were identified in the comparison of oeRIP2 vs. WT, oeRIP2 vs. shRIP2, and shRIP2 vs. WT, respectively. These DE AS genes participated in many important KEGG pathways, including regulation of autophagy, Wnt signaling pathway, Ubiquitin mediated proteolysis, MAPK signaling pathway, and Focal adhesion, etc. In conclusion, this research provided a broad atlas of the genome-wide scale of the AS event landscape in <i>RIP2</i> overexpression/knockdown and wild-type chicken macrophages. This research also provides the theoretical basis of the gene network related to <i>RIP2</i>.
DOI: 10.6084/m9.figshare.24310372
title: Met stimulates ARID1A degradation and activation of the PI3K-SREBP1 signaling to promote milk fat synthesis in bovine mammary epithelial cells

description: Methionine (Met) can promote milk fat synthesis in bovine mammary epithelial cells (BMECs), but the potential molecular mechanism is largely unknown. In this report, we aim to explore the role and molecular mechanism of AT-rich interaction domain 1A (ARID1A) in milk fat synthesis stimulated by Met. ARID1A knockdown and activation indicated that ARID1A negatively regulated the synthesis of triglycerides, cholesterol and free fatty acids and the formation of lipid droplets in BMECs. ARID1A also negatively regulated the phosphorylation of PI3K and AKT proteins, as well as the expression and maturation of SREBP1. Met stimulated the phosphorylation of PI3K and AKT proteins, as well as the expression and maturation of SREBP1, while ARID1A gene activation blocked the stimulatory effects of Met. We further found that ARID1A was located in the nucleus of BMECs, and Met reduced the nuclear localization and expression of ARID1A. ARID1A gene activation blocked the stimulation of <i>PI3K</i> and <i>SREBP1</i> mRNA expression by Met. In summary, our data suggests that ARID1A negatively regulates milk fat synthesis stimulated by Met in BMECs through inhibiting the PI3K-SREBP1 signaling pathway, which may provide some new perspectives for improving milk fat synthesis.
DOI: 10.6084/m9.figshare.24310372.v1
title: Met stimulates ARID1A degradation and activation of the PI3K-SREBP1 signaling to promote milk fat synthesis in bovine mammary epithelial cells

description: Methionine (Met) can promote milk fat synthesis in bovine mammary epithelial cells (BMECs), but the potential molecular mechanism is largely unknown. In this report, we aim to explore the role and molecular mechanism of AT-rich interaction domain 1A (ARID1A) in milk fat synthesis stimulated by Met. ARID1A knockdown and activation indicated that ARID1A negatively regulated the synthesis of triglycerides, cholesterol and free fatty acids and the formation of lipid droplets in BMECs. ARID1A also negatively regulated the phosphorylation of PI3K and AKT proteins, as well as the expression and maturation of SREBP1. Met stimulated the phosphorylation of PI3K and AKT proteins, as well as the expression and maturation of SREBP1, while ARID1A gene activation blocked the stimulatory effects of Met. We further found that ARID1A was located in the nucleus of BMECs, and Met reduced the nuclear localization and expression of ARID1A. ARID1A gene activation blocked the stimulation of <i>PI3K</i> and <i>SREBP1</i> mRNA expression by Met. In summary, our data suggests that ARID1A negatively regulates milk fat synthesis stimulated by Met in BMECs through inhibiting the PI3K-SREBP1 signaling pathway, which may provide some new perspectives for improving milk fat synthesis.
DOI: 10.6084/m9.figshare.23975276
title: Comparative muscle transcriptome of Mali and Hampshire breeds of pigs: a preliminary study

description: Muscle development is an important priority of pig breeding programs. There is a considerable variation in muscularity between the breeds, but the regulation mechanisms of genes underlying myogenesis are still unclear. Transcriptome data from two breeds of pigs with divergent muscularity (Mali and Hampshire) were integrated with histology, immunofluorescence and meat yield to identify differences in myogenesis during the early growth phase. The muscle transcriptomics analysis revealed 17,721 common, 1413 and 1115 unique transcripts to Hampshire and Mali, respectively. This study identified 908 differentially expressed genes (<i>p</i> &lt; 0.05; log<sub>2</sub>FC &gt; ±1) in the muscle samples, of which 550 were upregulated and 358 were downregulated in Hampshire pigs, indicating differences in physiological process related to muscle function and development. Expression of genes related to myoblast fusion (<i>MYMK</i>), skeletal muscle satellite cell proliferation (<i>ANGPT1</i>, <i>CDON</i>) and growth factors (<i>HGF, IGF1, IGF2</i>) were higher in Hampshire than Mali, even though transcript levels of several other myogenesis-related genes (<i>MYF6, MYOG, MSTN</i>) were similar. The number of fibers per fascicle and the expression of myogenic marker proteins (MYOD1, MYOG and PAX7) were more in Hampshire as compared to Mali breed of pig, supporting results of transcriptome studies. The results suggest that differences in muscularity between breeds could be related to the regulation of myoblast fusion and myogenic activities. The present study will help to identify genes that could be explored for their utility in the selection of animals with different muscularities.
DOI: 10.6084/m9.figshare.23975276.v1
title: Comparative muscle transcriptome of Mali and Hampshire breeds of pigs: a preliminary study

description: Muscle development is an important priority of pig breeding programs. There is a considerable variation in muscularity between the breeds, but the regulation mechanisms of genes underlying myogenesis are still unclear. Transcriptome data from two breeds of pigs with divergent muscularity (Mali and Hampshire) were integrated with histology, immunofluorescence and meat yield to identify differences in myogenesis during the early growth phase. The muscle transcriptomics analysis revealed 17,721 common, 1413 and 1115 unique transcripts to Hampshire and Mali, respectively. This study identified 908 differentially expressed genes (<i>p</i> &lt; 0.05; log<sub>2</sub>FC &gt; ±1) in the muscle samples, of which 550 were upregulated and 358 were downregulated in Hampshire pigs, indicating differences in physiological process related to muscle function and development. Expression of genes related to myoblast fusion (<i>MYMK</i>), skeletal muscle satellite cell proliferation (<i>ANGPT1</i>, <i>CDON</i>) and growth factors (<i>HGF, IGF1, IGF2</i>) were higher in Hampshire than Mali, even though transcript levels of several other myogenesis-related genes (<i>MYF6, MYOG, MSTN</i>) were similar. The number of fibers per fascicle and the expression of myogenic marker proteins (MYOD1, MYOG and PAX7) were more in Hampshire as compared to Mali breed of pig, supporting results of transcriptome studies. The results suggest that differences in muscularity between breeds could be related to the regulation of myoblast fusion and myogenic activities. The present study will help to identify genes that could be explored for their utility in the selection of animals with different muscularities.
DOI: 10.5281/zenodo.10703683
title: Supporting Information for: Ocean deoxygenation before the end-Permian mass extinction shown by secular variation of magnetic mineral assemblages

description: Supporting Information for:

Ocean deoxygenation before the end-Permian mass extinction shown by secular variation of magnetic mineral assemblages

The supporting information includes: (a) supplemental figures: Fig. S1, Rock magnetic experiments of selected sample; Fig. S2, Energy dispersive X-ray spectroscopy (EDXS) of Fe-oxide; Fig. S3, PAAS normalized rare earth element (REE) patterns; Fig. S4, Y/Ho ratio  and ΩCe vs. Th and Ti concentrations, respectively. (2) Measurement data: Table S1, Rock magnetic parameters of coercivity spectrum analysis; Table S2, Magnetic experiments results; and Table S3, the Rare Earth element results of the bulk carbonate samples
DOI: 10.5281/zenodo.7508664
title: Supporting Information for: Deoxygenation Prior to the End-Permian Mass Extinction: Evidence from Secular Variation of Magnetic Mineral Assemblage, Meishan Section, China

description: Supporting Information for:


Deoxygenation Prior to the End-Permian Mass Extinction: Evidence from Secular Variation of Magnetic Mineral Assemblage, Meishan Section, China


The supporting information includes: (a) supplemental figures: Figure S1, Rock magnetic experiments of selected sample and Figure S2, Energy dispersive X-ray spectroscopy (EDXS) of Fe-oxide; (2) measurement data: Table S1, Rock magnetic parameters of coercivity spectrum analysis and Table S2, Magnetic experiments results
DOI: 10.5281/zenodo.7647819
title: Supporting Information for: Deoxygenation Before the End-Permian Mass Extinction: Evidence from Secular Variation of Magnetic Mineral Assemblages, Meishan Section, China

description: Supporting Information for: <strong>Deoxygenation Before the End-Permian Mass Extinction: Evidence from Secular </strong><strong>Variation of Magnetic Mineral Assemblages, Meishan Section, China</strong> The supporting information includes: (a) supplemental figures: Figure S1, Rock magnetic experiments of selected sample and Figure S2, Energy dispersive X-ray spectroscopy (EDXS) of Fe-oxide; (2) measurement data: Table S1, Rock magnetic parameters of coercivity spectrum analysis and Table S2, Magnetic experiments results