cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26371456.v1
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.
DOI: 10.6084/m9.figshare.24681083
title: Candidate circRNAs related to skeletal muscle development in Dazu black goats

description: Circular RNA (CircRNA), as a classical noncoding RNA, has been proven to regulate skeletal muscle development (SMD). However, the molecular genetic basis of circRNA regulation in muscle cells remains unclear. In this study, the expression patterns of circRNAs in the longissimus dorsi muscle at embryonic day 75 and postnatal day 1 in DBGs were investigated to identify the key circRNAs that play an important role in SMD in goats. A total of 140 significantly and differentially expressed circRNAs (DEcircRNAs) were identified among the groups at different developmental stages. Among the 116 host genes (HGs) of DEcircRNAs, 76 were significantly and differentially expressed, which was confirmed by previous RNA_seq data. Furthermore, the expression pattern of 10 DEcircRNAs with RT-qPCR was verified, which showed 80% concordance rate with that of RNA_seq datasets. Moreover, the authenticity of seven randomly selected DEcircRNAs was verified by PCR Sanger sequencing. Based on the functional annotation results, among the 76 significantly and differentially expressed HGs, 74 were enriched in 845 GO terms, whereas 35 were annotated to 85 KEGG pathways. The results of this study could provide a comprehensive understanding of the genetic basis of circRNAs involved in SMD and muscle growth.
DOI: 10.6084/m9.figshare.24681083.v1
title: Candidate circRNAs related to skeletal muscle development in Dazu black goats

description: Circular RNA (CircRNA), as a classical noncoding RNA, has been proven to regulate skeletal muscle development (SMD). However, the molecular genetic basis of circRNA regulation in muscle cells remains unclear. In this study, the expression patterns of circRNAs in the longissimus dorsi muscle at embryonic day 75 and postnatal day 1 in DBGs were investigated to identify the key circRNAs that play an important role in SMD in goats. A total of 140 significantly and differentially expressed circRNAs (DEcircRNAs) were identified among the groups at different developmental stages. Among the 116 host genes (HGs) of DEcircRNAs, 76 were significantly and differentially expressed, which was confirmed by previous RNA_seq data. Furthermore, the expression pattern of 10 DEcircRNAs with RT-qPCR was verified, which showed 80% concordance rate with that of RNA_seq datasets. Moreover, the authenticity of seven randomly selected DEcircRNAs was verified by PCR Sanger sequencing. Based on the functional annotation results, among the 76 significantly and differentially expressed HGs, 74 were enriched in 845 GO terms, whereas 35 were annotated to 85 KEGG pathways. The results of this study could provide a comprehensive understanding of the genetic basis of circRNAs involved in SMD and muscle growth.
DOI: 10.6084/m9.figshare.27054804
title: Methylome and transcriptome joint analyses identify differentially expressed genes based on purebred and crossbred Tianjin-monkey Chicken

description: Tianjin-monkey Chicken is a locally bred naked neck poultry with limited population size. Herein, we intended to identify potential breed-related genes based on methylome and transcriptome analyses. Tianjin-monkey Chicken and Hy-line Brown Chicken were crossbred and the individuals were divided into three groups: PN (Purebred naked neck chicken(Tianjin-monkey Chicken)) group (n = 10); CN (Crossbred naked neck chicken) group (n = 10); CF (Crossbred feathered chicken) group (n = 10). These 30 individuals were subjected to whole genome bisulfite sequencing (WGBS) and transcriptome sequencing. Differential methylated regions were detected by WGBS. No significant difference existed in naked-neck-related traits between PN and CN chicken. CpG methylation level of the promoter region differed in PN, CN vs. CF chicken. By integrating methylome and transcriptome results, four genes were identified between PN and CN groups, and 24 key genes were identified between CN and CF groups, with great potential in breeding. The 24 genes were enriched on 32 GO terms and 3 KEGG pathways, such as ion transport. The promoter region CpG methylation level was distinct between feathered and naked neck groups. We identified 24 potential genes for future breeding, valuable for targeted breeding and genetic enhancement in poultry production.
DOI: 10.6084/m9.figshare.27054804.v1
title: Methylome and transcriptome joint analyses identify differentially expressed genes based on purebred and crossbred Tianjin-monkey Chicken

description: Tianjin-monkey Chicken is a locally bred naked neck poultry with limited population size. Herein, we intended to identify potential breed-related genes based on methylome and transcriptome analyses. Tianjin-monkey Chicken and Hy-line Brown Chicken were crossbred and the individuals were divided into three groups: PN (Purebred naked neck chicken(Tianjin-monkey Chicken)) group (n = 10); CN (Crossbred naked neck chicken) group (n = 10); CF (Crossbred feathered chicken) group (n = 10). These 30 individuals were subjected to whole genome bisulfite sequencing (WGBS) and transcriptome sequencing. Differential methylated regions were detected by WGBS. No significant difference existed in naked-neck-related traits between PN and CN chicken. CpG methylation level of the promoter region differed in PN, CN vs. CF chicken. By integrating methylome and transcriptome results, four genes were identified between PN and CN groups, and 24 key genes were identified between CN and CF groups, with great potential in breeding. The 24 genes were enriched on 32 GO terms and 3 KEGG pathways, such as ion transport. The promoter region CpG methylation level was distinct between feathered and naked neck groups. We identified 24 potential genes for future breeding, valuable for targeted breeding and genetic enhancement in poultry production.
DOI: 10.6084/m9.figshare.27960053
title: Single nucleotide polymorphisms of <i>GYS2</i> gene and its association with milk production traits of dairy cows

description: Glycogen synthase 2 (<i>GYS2</i>) encodes liver glycogen synthase, a rate limiting enzyme in glycogen metabolism. Our preliminary work suggested that <i>GYS2</i> was a candidate gene affecting milk production traits by analyzing the liver proteome of dairy cows. Herein, this research identified single nucleotide polymorphisms (SNPs) of <i>GYS2</i>, analyzed their genetic effects on traits of dairy cattle, and speculated the pathogenic mechanism through functional prediction of key mutation sites. Seven SNPs were found by resequencing and the association analysis showed that these SNPs were significantly associated with 305-day milk yield, fat yield, protein yield or fat percentage (<i>p</i>-value ≤ 0.0488). Six SNPs among them formed two haplotype blocks and they were associated with 305-day milk yield, fat yield, protein yield or fat percentage (<i>p</i>-value ≤ 0.0349). Furthermore, 5:g.88602007G &gt; A and 5:g.88602026G &gt; A were predicted to change the transcription factor binding sites (TFBSs), which might regulate the expression of <i>GYS2</i>. The missense mutation site, 5:g.88602535G &gt; T, changed the secondary structure of mRNA and the secondary and tertiary structure of protein. In summary, the <i>GYS2</i> was proved to have genetic effect on milk production traits, and its valuable seven SNPs, could provide more useful genetic information for molecular breeding of dairy cows.
DOI: 10.6084/m9.figshare.27960053.v1
title: Single nucleotide polymorphisms of <i>GYS2</i> gene and its association with milk production traits of dairy cows

description: Glycogen synthase 2 (<i>GYS2</i>) encodes liver glycogen synthase, a rate limiting enzyme in glycogen metabolism. Our preliminary work suggested that <i>GYS2</i> was a candidate gene affecting milk production traits by analyzing the liver proteome of dairy cows. Herein, this research identified single nucleotide polymorphisms (SNPs) of <i>GYS2</i>, analyzed their genetic effects on traits of dairy cattle, and speculated the pathogenic mechanism through functional prediction of key mutation sites. Seven SNPs were found by resequencing and the association analysis showed that these SNPs were significantly associated with 305-day milk yield, fat yield, protein yield or fat percentage (<i>p</i>-value ≤ 0.0488). Six SNPs among them formed two haplotype blocks and they were associated with 305-day milk yield, fat yield, protein yield or fat percentage (<i>p</i>-value ≤ 0.0349). Furthermore, 5:g.88602007G &gt; A and 5:g.88602026G &gt; A were predicted to change the transcription factor binding sites (TFBSs), which might regulate the expression of <i>GYS2</i>. The missense mutation site, 5:g.88602535G &gt; T, changed the secondary structure of mRNA and the secondary and tertiary structure of protein. In summary, the <i>GYS2</i> was proved to have genetic effect on milk production traits, and its valuable seven SNPs, could provide more useful genetic information for molecular breeding of dairy cows.
DOI: 10.6084/m9.figshare.24968736
title: A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses

description: Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.
DOI: 10.6084/m9.figshare.24968736.v1
title: A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses

description: Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.
DOI: 10.6084/m9.figshare.25325831
title: Multi-tissue gene expression profiling of cows with a genetic predisposition for low and high milk urea levels

description: Milk urea (MU) concentration is proposed as an indicator trait for breeding toward reduced nitrogen (N) emissions and leaching in dairy. We selected 20 German Holstein cows based on MU breeding values, with 10 cows each having low (LMUg) and high (HMUg) MU genetic predisposition. Using RNA-seq, we characterized these cows to unravel molecular pathways governing post-absorptive body N pools focusing on renal filtration and reabsorption of nitrogenous compounds, hepatic urea formation and mammary gland N excretion. While we observed minor adjustments in cellular energy metabolism in different tissues associated with different MU levels, no transcriptional differences in liver ammonia detoxification were detected, despite significant differences in MU between the groups. Differential expression of <i>AQP3</i> and <i>SLC38A2</i> in the kidney provides evidence for higher urea concentration in the collecting duct of LMU cows than HMU cows. The mammary gland exhibited the most significant differences, particularly in tricarboxylic acid (TCA) cycle genes, amino acid transport, tRNA binding, and casein synthesis. These findings suggest that selecting for lower MU could lead to altered urinary urea (UU) handling and changes in milk protein synthesis. However, given the genetic variability in N metabolism components, the long-term effectiveness of MU-based selection in reducing N emissions remains uncertain.
DOI: 10.6084/m9.figshare.25325831.v1
title: Multi-tissue gene expression profiling of cows with a genetic predisposition for low and high milk urea levels

description: Milk urea (MU) concentration is proposed as an indicator trait for breeding toward reduced nitrogen (N) emissions and leaching in dairy. We selected 20 German Holstein cows based on MU breeding values, with 10 cows each having low (LMUg) and high (HMUg) MU genetic predisposition. Using RNA-seq, we characterized these cows to unravel molecular pathways governing post-absorptive body N pools focusing on renal filtration and reabsorption of nitrogenous compounds, hepatic urea formation and mammary gland N excretion. While we observed minor adjustments in cellular energy metabolism in different tissues associated with different MU levels, no transcriptional differences in liver ammonia detoxification were detected, despite significant differences in MU between the groups. Differential expression of <i>AQP3</i> and <i>SLC38A2</i> in the kidney provides evidence for higher urea concentration in the collecting duct of LMU cows than HMU cows. The mammary gland exhibited the most significant differences, particularly in tricarboxylic acid (TCA) cycle genes, amino acid transport, tRNA binding, and casein synthesis. These findings suggest that selecting for lower MU could lead to altered urinary urea (UU) handling and changes in milk protein synthesis. However, given the genetic variability in N metabolism components, the long-term effectiveness of MU-based selection in reducing N emissions remains uncertain.
DOI: 10.5281/zenodo.17934978
title: LiDAR and Photogrammetry Point Clouds and R code for University of Padova courses on Geomatics for Forest and Environmental Sciences

description: Some examples of point clouds from lidar and photogrammetry, from drone and from helicopter surveys.

Esercizio.R is a file with a workflow in R for extracting trees from lidar point clouds using the lidR package.

These data are used in courses related to Geomatics applications to forest and environmental sciences for students at University of Padova, TESAF Department
DOI: 10.5281/zenodo.7421523
title: LiDAR and Photogrammetry Point Clouds and R code for University of Padova courses on Geomatics for Forest and Environmental Sciences

description: Some examples of point clouds from lidar and photogrammetry, from drone and from helicopter surveys.

Esercizio.R is a file with a workflow in R for extracting trees from lidar point clouds using the lidR package.

These data are used in courses related to Geomatics applications to forest and environmental sciences for students at University of Padova, TESAF Department
DOI: 10.6084/m9.figshare.30883673
title: Supporting information

description: Supporting information
DOI: 10.6084/m9.figshare.30883673.v2
title: Supporting information

description: Supporting information
DOI: 10.6084/m9.figshare.30883673.v1
title: Supporting information

description: Supporting information
DOI: 10.5281/zenodo.17937039
title: Optimizing selective baiting strategies for the wolf (Canis lupus)

description: We assessed the influence of bait height and type, with or without prey skin, on wolf (Canis lupus) consumption and species selectivity.
DOI: 10.5281/zenodo.17937036
title: Optimizing selective baiting strategies for the wolf (Canis lupus)

description: We assessed the influence of bait height and type, with or without prey skin, on wolf (Canis lupus) consumption and species selectivity.
DOI: 10.15468/dl.uvy64y
title: Occurrence Download

description: A dataset containing 46654372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2000-2023"
 ]
}

 The dataset includes 46654372 records from 348 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053189-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/ktsde4
title: Bredeweg te Kantens
title: Archeologisch bureauonderzoek

description: Archeologisch Bureauonderzoek aan de Brede weg te Kantens voor het plaatsen van tijdelijke woningen.
DOI: 10.15468/dl.4d4pm3
title: Occurrence Download

description: A dataset containing 98 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cicindela trisignata"
 ]
}

 The dataset includes 98 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053235-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57fheh
title: Occurrence Download

description: A dataset containing 111 records in GBIF matching the query:
SELECT "year", GBIF_EEARGCode( 1000, decimalLatitude, decimalLongitude, COALESCE(coordinateUncertaintyInMeters, 1000) ) AS eeaCellCode, classKey, class, genusKey, genus, COUNT(*) AS occurrences, MIN(COALESCE(coordinateUncertaintyInMeters, 1000)) AS minCoordinateUncertaintyInMeters, MIN(GBIF_TemporalUncertainty(eventDate, null)) AS minTemporalUncertainty FROM occurrence WHERE occurrenceStatus = 'PRESENT' AND genusKey IN (2284443, 2202786, 2161911, 2161467, 7652364, 2176168, 3092125, 2771094, 8782549, 2457378, 2453882, 2457825, 2454645, 2465626, 2466496, 2459675, 2444141, 2444221, 2447418, 2441658, 2442664, 3266899, 2473221, 2445496, 5221394, 2443339, 4553469) AND countrycode = 'BE' AND "year" &gt;= 1900 AND hasCoordinate = TRUE AND genusKey IS NOT NULL AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID') AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH') AND (LOWER(identificationVerificationStatus) NOT IN ( 'unverified', 'unvalidated', 'not validated', 'under validation', 'not able to validate', 'control could not be conclusive due to insufficient knowledge', 'uncertain', 'unconfirmed', 'unconfirmed - not reviewed', 'validation requested' ) OR identificationVerificationStatus IS NULL) AND COALESCE(coordinateUncertaintyInMeters, 1000) &lt;= 10000 GROUP BY "year", eeaCellCode, classKey, class, genusKey, genus ORDER BY "year" DESC, eeaCellCode ASC, genusKey ASC;

 The dataset's 111 records were derived from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053231-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uqccet
title: Occurrence Download

description: A dataset containing 511 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cylindera trisignata"
 ]
}

 The dataset includes 511 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053236-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mz8dpy
title: Occurrence Download

description: A dataset containing 2 records in GBIF matching the query:
SELECT "year", GBIF_EEARGCode( 1000, decimalLatitude, decimalLongitude, COALESCE(coordinateUncertaintyInMeters, 1000) ) AS eeaCellCode, classKey, class, familyKey, family, COUNT(*) AS occurrences, MIN(COALESCE(coordinateUncertaintyInMeters, 1000)) AS minCoordinateUncertaintyInMeters, MIN(GBIF_TemporalUncertainty(eventDate, null)) AS minTemporalUncertainty FROM occurrence WHERE occurrenceStatus = 'PRESENT' AND countrycode = 'BE' AND "year" &gt;= 1900 AND hasCoordinate = TRUE AND familyKey IS NOT NULL AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE') AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID') AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH') AND (LOWER(identificationVerificationStatus) NOT IN ( 'unverified', 'unvalidated', 'not validated', 'under validation', 'not able to validate', 'control could not be conclusive due to insufficient knowledge', 'uncertain', 'unconfirmed', 'unconfirmed - not reviewed', 'validation requested' ) OR identificationVerificationStatus IS NULL)AND familyKey IN (5666)AND COALESCE(coordinateUncertaintyInMeters, 1000) &lt;= 10000GROUP BY "year", eeaCellCode, classKey, class, familyKey, family ORDER BY "year" DESC, eeaCellCode ASC, familyKey ASC;

 The dataset's 2 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053230-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.