cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10606575
title: WGS of SC5314x529L parasexual progeny

description: SC5314 and 529L were mated to one another and concerted chromosome loss was induced by plating on pre-sporulation agar medium at 37C for 7 days. Colonies were screened for ploidy by flow cytometry. Cells were cultured overnight in YPD at 30 °C and genomic DNA for each strain was isolated from ~108 cells using the Zymo Research Quick-DNA™ Fungal/Bacterial Miniprep Kit according to the manufacturer’s instructions (Zymo, Irvine, CA). DNA libraries were prepared using NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). Prepared libraries were sequenced for 150 bp paired-end reads on an Illumina Novaseq platform at the Novogene Sequencing Facility. The reads were trimmed using trimmomatic 0.39 (with default parameters except slidingwindow:4:30, maxinfo:100:1, headcrop:12, and minlen:50) to get rid of the adaptor content in the sequences Using bowtie2 v2.2.6, the trimmed reads were aligned against the SC5314 reference genome (version A21-s02-m09-r10) obtained from the Candida Genome Database (www.candidagenome.org). The aligned SAM files were then converted to the BAM format using samtools v1.7.
DOI: 10.5281/zenodo.10606576
title: WGS of SC5314x529L parasexual progeny

description: SC5314 and 529L were mated to one another and concerted chromosome loss was induced by plating on pre-sporulation agar medium at 37C for 7 days. Colonies were screened for ploidy by flow cytometry. Cells were cultured overnight in YPD at 30 °C and genomic DNA for each strain was isolated from ~108 cells using the Zymo Research Quick-DNA™ Fungal/Bacterial Miniprep Kit according to the manufacturer’s instructions (Zymo, Irvine, CA). DNA libraries were prepared using NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). Prepared libraries were sequenced for 150 bp paired-end reads on an Illumina Novaseq platform at the Novogene Sequencing Facility. The reads were trimmed using trimmomatic 0.39 (with default parameters except slidingwindow:4:30, maxinfo:100:1, headcrop:12, and minlen:50) to get rid of the adaptor content in the sequences Using bowtie2 v2.2.6, the trimmed reads were aligned against the SC5314 reference genome (version A21-s02-m09-r10) obtained from the Candida Genome Database (www.candidagenome.org). The aligned SAM files were then converted to the BAM format using samtools v1.7.
DOI: 10.6084/m9.figshare.16847671
title: Table S2 Full count data.xlsx

description: Supplementary Table 1, containing information on all counts of microfilariae or L3's collected as part of the associated manuscript. Full details on data 
generation are available in the related manuscript.
DOI: 10.5281/zenodo.10605455
title: Data and code supporting analysis of the climate sensitivity of recharge

description: This code and data are used to generate the primary findings outlined in the article by Berghuijs et al. (2024), titled "Groundwater recharge is sensitive to changing long-term aridity," published in Nature Climate Change. The climate projections derived from CMIP6 are presented in Jaramillo et al. (2022). Recharge and aridity data need to be downloaded from their original sources, cited in the main paper.

References

Jaramillo, F., Piemontese, L., Berghuijs, W. R., Wang‐Erlandsson, L., Greve, P., & Wang, Z. (2022). Fewer Basins Will Follow Their Budyko Curves Under Global Warming and Fossil‐Fueled Development. Water Resources Research, 58(8), e2021WR031825.
DOI: 10.5281/zenodo.10605454
title: Data and code supporting analysis of the climate sensitivity of recharge

description: This code and data are used to generate the primary findings outlined in the article by Berghuijs et al. (2024), titled "Groundwater recharge is sensitive to changing long-term aridity," published in Nature Climate Change. The climate projections derived from CMIP6 are presented in Jaramillo et al. (2022). Recharge and aridity data need to be downloaded from their original sources, cited in the main paper.

References

Jaramillo, F., Piemontese, L., Berghuijs, W. R., Wang‐Erlandsson, L., Greve, P., & Wang, Z. (2022). Fewer Basins Will Follow Their Budyko Curves Under Global Warming and Fossil‐Fueled Development. Water Resources Research, 58(8), e2021WR031825.
DOI: 10.6084/m9.figshare.16847707
title: Table S3 edgeR results.xlsx

description: Supplementary table 2, containing full results from edgeR RNA-sequencing differential expression analysis of <i>B. malayi </i>microfilariae controls compared to treatment with tetracyclines, used in the associated manuscript for drawing conclusions. Full details on data 
generation are available in the related manuscript.<br>
DOI: 10.6084/m9.figshare.22603358.v1
title: Additional file 6 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 6: Supplementary Table S5. Differentially accessible peaks between 7 distinct sub-clusters of myogenic cells in scATAC-seq data. Related to Figure 4.
DOI: 10.6084/m9.figshare.22603364
title: Additional file 8 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 8: Supplementary Table S7. Full list of cell type-specific motif enrichment. Related to Figure 5.
DOI: 10.6084/m9.figshare.22603346.v1
title: Additional file 2 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 2: Supplementary Table S1. DEG between 31 distinct cell clusters in scRNA-seq data after ambient RNA cleaning. Related to Figure 1.
DOI: 10.5281/zenodo.10630205
title: cynoglossus_puncticeps_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10630206
title: cynoglossus_puncticeps_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.22603370
title: Additional file 10 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 10: Supplementary Table S9. The top 10 regulons and respective target genes inferred by SCENIC. Related to Figure 5.
DOI: 10.6084/m9.figshare.22603349
title: Additional file 3 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 3: Supplementary Table S2. Gene Ontology analysis of the DEGs for each cell type. Related to Figure S2.
DOI: 10.6084/m9.figshare.22603373.v1
title: Additional file 11 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 11: Supplementary Table S10. The complete list of regulons and their respective predicted target genes inferred by SCENIC. Related to Figure 5.
DOI: 10.6084/m9.figshare.16847719
title: Table S4 TopGO enrichment results.xlsx

description: Supplementary table 3, containing the full results of Gene Ontology enrichment analysis using statistically significantly up- and down-regulated genes from Supplementary table 2. This data comes from <i>B. malayi</i> microfilariae before and after treatment with tetracycline to remove the <i>Wolbachia</i> endosymbiont . Full details on data generation are available in the related manuscript.<br>
DOI: 10.6084/m9.figshare.22603367
title: Additional file 9 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 9: Supplementary Table S8. Expression of transcription factors associated with cell type-specific motif enrichment. Related to Figure 5.
DOI: 10.6084/m9.figshare.22603367.v1
title: Additional file 9 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 9: Supplementary Table S8. Expression of transcription factors associated with cell type-specific motif enrichment. Related to Figure 5.
DOI: 10.60520/ieda/113124
title: Young silicic rocks of the Greater Caucasus

description: Rhyolites and granites of the Pliocene-Pleistocene age exposed in the collision zone of the Greater Caucasus, Russia. Includes ignimbrites and lavas associated with the Chegem caldera (2.9 Ma) and Elbrus volcano (1.98, 0.7 Ma and youger) and rhyolitic necks and granites in Tyrnyauz (1.98 Ma).
description: Shcherbakov, V., Bindeman, I., & Gazeev, V. (2022). Geochemical, Isotopic and Petrological Constraints on the Origin and Evolution of the Recent Silicic Magmatism of the Greater Caucasus. Minerals, 12(1), Article 1.
DOI: 10.6084/m9.figshare.22603349.v1
title: Additional file 3 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 3: Supplementary Table S2. Gene Ontology analysis of the DEGs for each cell type. Related to Figure S2.
DOI: 10.6084/m9.figshare.22603370.v1
title: Additional file 10 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 10: Supplementary Table S9. The top 10 regulons and respective target genes inferred by SCENIC. Related to Figure 5.
DOI: 10.6084/m9.figshare.22603346
title: Additional file 2 of Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

description: Additional file 2: Supplementary Table S1. DEG between 31 distinct cell clusters in scRNA-seq data after ambient RNA cleaning. Related to Figure 1.
DOI: 10.6084/m9.figshare.1591920.v2
title: Abundance and Diversity of insects- Lab4--Experimental Design

description: This experiment was conducted in 6 different locations, over the course of 2 days. The field experiment consisted of 5 group members, D. Hosseini J. Chera, M. Francetic and N. Maximin at York University. Two data set was collected in total, the first data set was collected on October 14th, and the second was collected on October 21st. The purpose of this experiment was to compare and contrast the abundance and distribution of insects between high and low human traffic areas (High traffic area means areas with the most population in the York University in contrast low traffic area means woodlot, or grassland). The 3 high human traffic areas are: in front of Vari Hall, between Lumbers and Lassonde, and campus walk (which is in front of Stong) and the 3 low traffic areas are: Danby woodlot, Osgoode woodlot and Stong woodlot. 10 pan traps, each spaced equally from each other were placed at each location. The pan traps were set for an hour from the time it was placed, after which the group members observed, counted and documented the insects captured. The same process was repeated for a second time a week later. A total of 60 pan traps were placed each day, adding to a total of 120 pan traps for both days. Note: The color of the pan traps was not under consideration, meaning the colors did not matter to the experiment.
DOI: 10.6084/m9.figshare.1591904
title: Factors Affecting Species Richness in Grassland and Woodlots at York University

description: Data was collected on October 1, October 8, and October 15, 2015 at York University, Keele Campus. Three grasslands (Boynton, Danby, Stong) and three woodlots (Boyer, Boynton, Danby) were sampled each day. Grasslands and woodlots chosen were required to be physically separated from other samples of their own type by either a road or a building. An uninterrupted area of 50m² was chosen from each grassland and woodlot, and divided into 100 quadrats of 5m² which were numbered from 1 to 100. Three quadrats per habitat were chosen for sampling using a random number table. To sample a quadrat, transect tapes were laid at its perimeter and every plant within the quadrat and touching the transect tapes was identified to species and classified into a functional group using flower and tree guides. Total number of plants of each species was also recorded. Grasses (graminoids) were an exception as they were not identified to species but total number of species was counted.
DOI: 10.6084/m9.figshare.1591904.v1
title: Factors Affecting Species Richness in Grassland and Woodlots at York University

description: Data was collected on October 1, October 8, and October 15, 2015 at York University, Keele Campus. Three grasslands (Boynton, Danby, Stong) and three woodlots (Boyer, Boynton, Danby) were sampled each day. Grasslands and woodlots chosen were required to be physically separated from other samples of their own type by either a road or a building. An uninterrupted area of 50m² was chosen from each grassland and woodlot, and divided into 100 quadrats of 5m² which were numbered from 1 to 100. Three quadrats per habitat were chosen for sampling using a random number table. To sample a quadrat, transect tapes were laid at its perimeter and every plant within the quadrat and touching the transect tapes was identified to species and classified into a functional group using flower and tree guides. Total number of plants of each species was also recorded. Grasses (graminoids) were an exception as they were not identified to species but total number of species was counted.
DOI: 10.6084/m9.figshare.1591905.v2
title: Week 7 Field Data: Population and Abundance of Birds at York University

description: Data for this field experiment was collected over 2 days; October 13th, 2015 and October 20th, 2015. On October 13th, the environmental conditions were windy, heavily clouded, and humid, with a temperature of 15 degrees Celsius. On October 20th, the environmental conditions were windy, cloudy, and light precipitation, with a temperature of 17 degrees Celsius. Data was recorded on the Keele Campus of York University in grasslands, woodlots, and urban areas. The field experiment involved laying 8-10 transects in urban areas and 8-10 transects in natural areas. An urban area was defined as having at least 75% manmade materials (pavement, buildings, etc,) and a natural area was defined as having at least 75% vegetation on the earth. Once these 120 metre transects were placed, birds within the length of the transect were recorded. The vicinity of the birds in relation to the transect was 20-30 metres on each side and 15 metres vertically. Birds who entered the vicinity more than once were only recorded once. This method was repeated for each transect.
DOI: 10.6084/m9.figshare.1591901
title: Levels of human traffic effecting the abundance of insects

description: This experiment was conducted in a group of five members who are J. Chera, D. Hosseini, M. Francetic and N. Maximin for two days at York University. The first data set was collected on October 14, 2015 from 2:30-4:30pm and the second data set was collected on October 20, 2015 from 2:30-4:30pm. Note that on both days it was cloudy with little sun exposure. The purpose of this experiment was to determine if different traffic levels of humans affect the abundance and diversity of insects. This experiment took place in six different locations where three of the locations had high human traffic, which are in front of Vari Hall, between Lumbers and Lassonde and campus walk (infront of stong). The other three locations had low human traffic, which are Danby woodlot, Osgoode woodlot and Stong woodlot. In each location, 10 pan traps were placed spaced from each other, and left at each location for an hour from the time it was placed. After an hour had passed, the pan traps were observed to see what type of insects were found and then the number of each insect was recorded. Therefore a total of 60 pan traps were placed on both days, for a total of 120 pan traps. This procedure was then replicated for the second day. It should be noted that the color of the pan trap does not matter for this experiment.
DOI: 10.6084/m9.figshare.1591920.v3
title: Abundance and Diversity of insects- Lab4--Experimental Design

description: This experiment was conducted in 6 different locations, over the course of 2 days. The field experiment consisted of 5 group members, D. Hosseini J. Chera, M. Francetic and N. Maximin at York University. Two data set was collected in total, the first data set was collected on October 14th, and the second was collected on October 21st. The purpose of this experiment was to compare and contrast the abundance and distribution of insects between high and low human traffic areas (High traffic area means areas with the most population in the York University in contrast low traffic area means woodlot, or grassland). The 3 high human traffic areas are: in front of Vari Hall, between Lumbers and Lassonde, and campus walk (which is in front of Stong) and the 3 low traffic areas are: Danby woodlot, Osgoode woodlot and Stong woodlot. 10 pan traps, each spaced equally from each other were placed at each location. The pan traps were set for an hour from the time it was placed, after which the group members observed, counted and documented the insects captured. The same process was repeated for a second time a week later. A total of 60 pan traps were placed each day, adding to a total of 120 pan traps for both days. Note: The color of the pan traps was not under consideration, meaning the colors did not matter to the experiment.
DOI: 10.6084/m9.figshare.1591905.v1
title: Week 7 Field Data: Population and Abundance of Birds at York University

description: Data for this field experiment was collected over 2 days; October 13th, 2015 and October 20th, 2015. On October 13th, the environmental conditions were windy, heavily clouded, and humid, with a temperature of 15 degrees Celsius. On October 20th, the environmental conditions were windy, cloudy, and light precipitation, with a temperature of 17 degrees Celsius. Data was recorded on the Keele Campus of York University in grasslands, woodlots, and urban areas. The field experiment involved laying 8-10 transects in urban areas and 8-10 transects in natural areas. An urban area was defined as having at least 75% manmade materials (pavement, buildings, etc,) and a natural area was defined as having at least 75% vegetation on the earth. Once these 120 metre transects were placed, birds within the length of the transect were recorded. The vicinity of the birds in relation to the transect was 20-30 metres on each side and 15 metres vertically. Birds who entered the vicinity more than once were only recorded once. This method was repeated for each transect.
DOI: 10.6084/m9.figshare.1591920.v4
title: Abundance and Diversity of insects- Lab4--Experimental Design

description: This experiment was conducted in 6 different locations, over the course of 2 days. The field experiment was conducted at York University; consisted of 5 group members, D. Hosseini J. Chera, M. Francetic and N. Maximin. Two data set was collected in total, the first data set was collected on October 14th, and the second was collected on October 21st. The purpose of this experiment was to compare and contrast the abundance and distribution of insects between high and low human traffic areas (High traffic area means areas with the most population in the York University in contrast low traffic area means woodlot, or grassland). The 3 high human traffic areas are: in front of Vari Hall, between Lumbers and Lassonde, and campus walk (which is in front of Stong) and the 3 low traffic areas are: Danby woodlot, Osgoode woodlot and Stong woodlot. 10 pan traps, each spaced equally from each other were placed at each location. The pan traps were set for an hour from the time it was placed, after which the group members observed, counted and documented the insects captured. The same process was repeated for a second time a week later. A total of 60 pan traps were placed each day, adding to a total of 120 pan traps for both days. Note: The color of the pan traps was not under consideration, meaning the colors did not matter to the experiment.
DOI: 10.6084/m9.figshare.1591901.v1
title: Levels of human traffic effecting the abundance of insects

description: This experiment was conducted in a group of five members who are J. Chera, D. Hosseini, M. Francetic and N. Maximin for two days at York University. The first data set was collected on October 14, 2015 from 2:30-4:30pm and the second data set was collected on October 20, 2015 from 2:30-4:30pm. Note that on both days it was cloudy with little sun exposure. The purpose of this experiment was to determine if different traffic levels of humans affect the abundance and diversity of insects. This experiment took place in six different locations where three of the locations had high human traffic, which are in front of Vari Hall, between Lumbers and Lassonde and campus walk. The other three locations had low human traffic, which are Danby woodlot, Osgoode woodlot and Stong woodlot. In each location, 10 pan traps were placed spaced from each other, and left at each location for an hour from the time it was placed. After an hour had passed, the pan traps were observed to see what type of insects were found and then the number of each insect was recorded. Therefore a total of 60 pan traps were placed on both days, for a total of 120 pan traps. This procedure was then replicated for the second day. It should be noted that the color of the pan trap does not matter for this experiment.
DOI: 10.6084/m9.figshare.1591920.v6
title: Abundance and Diversity of insects- Lab4--Experimental Design

description: This experiment was conducted in 6 different locations, over the course of 2 days. The field experiment was conducted at York University; consisted of 5 group members, D. Hosseini J. Chera, M. Francetic and N. Maximin. Two data set was collected in total, the first data set was collected on October 14th, and the second was collected on October 21st. The purpose of this experiment was to compare and contrast the abundance and distribution of insects between high and low human traffic areas (High traffic area means areas with the most population in the York University in contrast low traffic area means woodlot, or grassland). The 3 high human traffic areas are: in front of Vari Hall, between Lumbers and Lassonde, and campus walk (which is in front of Stong) and the 3 low traffic areas are: Danby woodlot, Osgoode woodlot and Stong woodlot. 10 pan traps, each spaced equally from each other were placed at each location. The pan traps were set for an hour from the time it was placed, after which the group members observed, counted and documented the insects captured. The same process was repeated for a second time a week later. A total of 60 pan traps were placed each day, adding to a total of 120 pan traps for both days. Note: The color of the pan traps was not under consideration, meaning the colors did not matter to the experiment.
DOI: 10.6084/m9.figshare.1591901.v2
title: Levels of human traffic effecting the abundance of insects

description: This experiment was conducted in a group of five members who are J. Chera, D. Hosseini, M. Francetic and N. Maximin for two days at York University. The first data set was collected on October 14, 2015 from 2:30-4:30pm and the second data set was collected on October 20, 2015 from 2:30-4:30pm. Note that on both days it was cloudy with little sun exposure. The purpose of this experiment was to determine if different traffic levels of humans affect the abundance and diversity of insects. This experiment took place in six different locations where three of the locations had high human traffic, which are in front of Vari Hall, between Lumbers and Lassonde and campus walk (infront of stong). The other three locations had low human traffic, which are Danby woodlot, Osgoode woodlot and Stong woodlot. In each location, 10 pan traps were placed spaced from each other, and left at each location for an hour from the time it was placed. After an hour had passed, the pan traps were observed to see what type of insects were found and then the number of each insect was recorded. Therefore a total of 60 pan traps were placed on both days, for a total of 120 pan traps. This procedure was then replicated for the second day. It should be noted that the color of the pan trap does not matter for this experiment.