cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6181619
title: MOESM3 of Modelling steroidogenesis: a framework model to support hypothesis generation and testing across endocrine studies

description: Additional file 3. Editable Graphml file of a framework model of rat Leydig cell steroidogenesis.
DOI: 10.6084/m9.figshare.6181619.v1
title: MOESM3 of Modelling steroidogenesis: a framework model to support hypothesis generation and testing across endocrine studies

description: Additional file 3. Editable Graphml file of a framework model of rat Leydig cell steroidogenesis.
DOI: 10.6084/m9.figshare.6181601
title: MOESM3 of Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

description: Additional file 3. This file contains all supplementary tables relating to lncRNA identification via the conservation of synteny. Table S3. lncRNAs inferred in one species by the genomic alignment of a transcript assembled with the RNA-seq libraries from a related spdecies. Table S12. Presence of intergenic lncRNAs both in sheep and cattle, in regions of conserved synteny. Table S13. Presence of intergenic lncRNAs both in sheep and goat, in regions of conserved synteny. Table S14. Presence of intergenic lncRNAs both in cattle and goat, in regions of conserved synteny. Table S15. Presence of intergenic lncRNAs both in sheep and humans, in regions of conserved synteny. Table S16. Presence of intergenic lncRNAs both in goat and humans, in regions of conserved synteny. Table S17. Presence of intergenic lncRNAs both in cattle and humans, in regions of conserved synteny. Table S18. High-confidence lncRNA pairs, those conserved across species both sequentially and positionally.
DOI: 10.6084/m9.figshare.6181601.v1
title: MOESM3 of Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

description: Additional file 3. This file contains all supplementary tables relating to lncRNA identification via the conservation of synteny. Table S3. lncRNAs inferred in one species by the genomic alignment of a transcript assembled with the RNA-seq libraries from a related spdecies. Table S12. Presence of intergenic lncRNAs both in sheep and cattle, in regions of conserved synteny. Table S13. Presence of intergenic lncRNAs both in sheep and goat, in regions of conserved synteny. Table S14. Presence of intergenic lncRNAs both in cattle and goat, in regions of conserved synteny. Table S15. Presence of intergenic lncRNAs both in sheep and humans, in regions of conserved synteny. Table S16. Presence of intergenic lncRNAs both in goat and humans, in regions of conserved synteny. Table S17. Presence of intergenic lncRNAs both in cattle and humans, in regions of conserved synteny. Table S18. High-confidence lncRNA pairs, those conserved across species both sequentially and positionally.
DOI: 10.6084/m9.figshare.6181592
title: MOESM1 of Modelling steroidogenesis: a framework model to support hypothesis generation and testing across endocrine studies

description: Additional file 1. Editable Graphml file of a framework model of human steroidogenesis.
DOI: 10.6084/m9.figshare.6181592.v1
title: MOESM1 of Modelling steroidogenesis: a framework model to support hypothesis generation and testing across endocrine studies

description: Additional file 1. Editable Graphml file of a framework model of human steroidogenesis.
DOI: 10.6084/m9.figshare.6181589
title: Additional file 23: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Pan-genome fasta for Lactobacillus plantarum (Fasta). (FASTA 5115 kb)
DOI: 10.6084/m9.figshare.6181574
title: Additional file 22: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Core-genome fasta for Lactobacillus plantarum (Fasta). (FASTA 193 kb)
DOI: 10.6084/m9.figshare.6181574.v1
title: Additional file 22: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Core-genome fasta for Lactobacillus plantarum (Fasta). (FASTA 193 kb)
DOI: 10.6084/m9.figshare.6181571
title: MOESM2 of Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

description: Additional file 2. This file contains all supplementary tables relating to the characterisation of goat lncRNAs. Table S2. Candidate goat lncRNAs: a shortlist of novel gene models assessed for coding potential using CPC, CPAT, PLEK, blastp vs. Swiss-Prot, and HMMER vs. Pfam. Table S5. Goat gene models considered non-coding by either CPC, CPAT or PLEK but showing sequence homology to either a known protein (in Swiss-Prot) or protein domain (in Pfam-A). Table S7. Number of novel goat lncRNA gene models identified per chromosome. Table S9. Number of novel goat lncRNA gene models identified, by category. Table S11. Alignments of novel goat lncRNA gene models to sheep, cattle and human lncRNA. Table S20. Expression level estimates for 4392 novel goat lncRNAs, as transcripts per million (TPM), which were assessed using 54 RNA-seq libraries (20 tissues plus one cell type under two different conditions, for each sample four individuals were sequenced).
DOI: 10.6084/m9.figshare.6181571.v1
title: MOESM2 of Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

description: Additional file 2. This file contains all supplementary tables relating to the characterisation of goat lncRNAs. Table S2. Candidate goat lncRNAs: a shortlist of novel gene models assessed for coding potential using CPC, CPAT, PLEK, blastp vs. Swiss-Prot, and HMMER vs. Pfam. Table S5. Goat gene models considered non-coding by either CPC, CPAT or PLEK but showing sequence homology to either a known protein (in Swiss-Prot) or protein domain (in Pfam-A). Table S7. Number of novel goat lncRNA gene models identified per chromosome. Table S9. Number of novel goat lncRNA gene models identified, by category. Table S11. Alignments of novel goat lncRNA gene models to sheep, cattle and human lncRNA. Table S20. Expression level estimates for 4392 novel goat lncRNAs, as transcripts per million (TPM), which were assessed using 54 RNA-seq libraries (20 tissues plus one cell type under two different conditions, for each sample four individuals were sequenced).
DOI: 10.6084/m9.figshare.6181547
title: MOESM1 of Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

description: Additional file 1. This file contains all supplementary tables relating to the characterisation of sheep lncRNAs. Table S1. Candidate sheep lncRNAs: a shortlist of novel gene models (plus independently confirmed known gene models) assessed for coding potential using CPC, CPAT, PLEK, blastp vs. Swiss-Prot, and HMMER vs. Pfam. Table S4. Sheep gene models considered as non-coding by either CPC, CPAT or PLEK but showing sequence homology to either a known protein (in Swiss-Prot) or protein domain (in Pfam-A). Table S6. Number of novel sheep lncRNA gene models identified per chromosome. Table S8. Number of novel sheep lncRNA gene models identified, by category. Table S10. Alignments of novel sheep lncRNA gene models to goat, cattle and human lncRNA. Table S19. Expression level estimates for 13,047 novel sheep lncRNAs, as transcripts per million (TPM), which were assessed using 71 adult RNA-seq libraries (11 tissues plus one cell type under two conditions, each sample is sequenced for six individuals). Table S21. Reproducibility of sheep lncRNA gene models when merging all combinations of data from six adults (three females and three males), for each individual a common set of RNA-seq libraries (comprising 31 tissues/cell types) was available. Table S22. Number of sheep expression atlas RNA-seq libraries (out of 429 in total) for which a candidate lncRNA gene model cannot be fully reconstructed. Table S23. Genes within each co-expression cluster, after network analysis of the sheep RNA-seq libraries. Table S24. Number of sheep lncRNAs co-expressed with protein-coding genes. Table S25. Distance between lncRNAs and protein-coding genes within the same co-expression cluster, on the same chromosome, for sheep. Table S26. Correlation between the expression profile of sheep lncRNAs and their nearest protein-coding genes, both 5′ and 3′.
DOI: 10.6084/m9.figshare.6181547.v1
title: MOESM1 of Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

description: Additional file 1. This file contains all supplementary tables relating to the characterisation of sheep lncRNAs. Table S1. Candidate sheep lncRNAs: a shortlist of novel gene models (plus independently confirmed known gene models) assessed for coding potential using CPC, CPAT, PLEK, blastp vs. Swiss-Prot, and HMMER vs. Pfam. Table S4. Sheep gene models considered as non-coding by either CPC, CPAT or PLEK but showing sequence homology to either a known protein (in Swiss-Prot) or protein domain (in Pfam-A). Table S6. Number of novel sheep lncRNA gene models identified per chromosome. Table S8. Number of novel sheep lncRNA gene models identified, by category. Table S10. Alignments of novel sheep lncRNA gene models to goat, cattle and human lncRNA. Table S19. Expression level estimates for 13,047 novel sheep lncRNAs, as transcripts per million (TPM), which were assessed using 71 adult RNA-seq libraries (11 tissues plus one cell type under two conditions, each sample is sequenced for six individuals). Table S21. Reproducibility of sheep lncRNA gene models when merging all combinations of data from six adults (three females and three males), for each individual a common set of RNA-seq libraries (comprising 31 tissues/cell types) was available. Table S22. Number of sheep expression atlas RNA-seq libraries (out of 429 in total) for which a candidate lncRNA gene model cannot be fully reconstructed. Table S23. Genes within each co-expression cluster, after network analysis of the sheep RNA-seq libraries. Table S24. Number of sheep lncRNAs co-expressed with protein-coding genes. Table S25. Distance between lncRNAs and protein-coding genes within the same co-expression cluster, on the same chromosome, for sheep. Table S26. Correlation between the expression profile of sheep lncRNAs and their nearest protein-coding genes, both 5′ and 3′.
DOI: 10.6084/m9.figshare.6181529
title: Additional file 3: of Influence of climate on tree mortality in taiwania (Taiwania cryptomerioides) stands in Taiwan

description: Climate data. (CSV 2.49 kb)
DOI: 10.6084/m9.figshare.6181529.v1
title: Additional file 3: of Influence of climate on tree mortality in taiwania (Taiwania cryptomerioides) stands in Taiwan

description: Climate data. (CSV 2.49 kb)
DOI: 10.6084/m9.figshare.6181517
title: Additional file 1: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: All strains used for core- and pan-genome analysis study. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6181517.v1
title: Additional file 1: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: All strains used for core- and pan-genome analysis study. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6181508
title: Additional file 2: of Influence of climate on tree mortality in taiwania (Taiwania cryptomerioides) stands in Taiwan

description: Mensuration data for the plots in Compartment 12. (CSV 547 kb)
DOI: 10.6084/m9.figshare.6181508.v1
title: Additional file 2: of Influence of climate on tree mortality in taiwania (Taiwania cryptomerioides) stands in Taiwan

description: Mensuration data for the plots in Compartment 12. (CSV 547 kb)
DOI: 10.6084/m9.figshare.6181490
title: Additional file 3: of Effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose tissue in Holstein-Friesian bulls

description: Genes differentially expressed in the subcutaneous adipose of Holstein-Friesian dairy bulls fed on low plane of nutrition in comparison to high plane of nutrition, slaughtered at 18 weeks of age. Genes outlined by the Molecule Activity Predictor function in IPA. (XLS 106 kb)
DOI: 10.6084/m9.figshare.6181490.v1
title: Additional file 3: of Effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose tissue in Holstein-Friesian bulls

description: Genes differentially expressed in the subcutaneous adipose of Holstein-Friesian dairy bulls fed on low plane of nutrition in comparison to high plane of nutrition, slaughtered at 18 weeks of age. Genes outlined by the Molecule Activity Predictor function in IPA. (XLS 106 kb)
DOI: 10.6084/m9.figshare.6181484
title: Additional file 1: of Influence of climate on tree mortality in taiwania (Taiwania cryptomerioides) stands in Taiwan

description: Mensuration data for the plots in Compartment 3. (CSV 303 kb)
DOI: 10.6084/m9.figshare.6181484.v1
title: Additional file 1: of Influence of climate on tree mortality in taiwania (Taiwania cryptomerioides) stands in Taiwan

description: Mensuration data for the plots in Compartment 3. (CSV 303 kb)
DOI: 10.6084/m9.figshare.6181448
title: Additional file 16: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Pan-genome fasta for Lactobacillus reuteri (Fasta). (FASTA 2283 kb)
DOI: 10.6084/m9.figshare.6181448.v1
title: Additional file 16: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Pan-genome fasta for Lactobacillus reuteri (Fasta). (FASTA 2283 kb)
DOI: 10.6084/m9.figshare.6181430
title: Additional file 15: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Core-genome fasta for Lactobacillus reuteri (Fasta). (FASTA 312 kb)
DOI: 10.6084/m9.figshare.6181430.v1
title: Additional file 15: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Core-genome fasta for Lactobacillus reuteri (Fasta). (FASTA 312 kb)
DOI: 10.6084/m9.figshare.6181382
title: Additional file 12 of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Potential HGT in Lactobacillus delbrueckii. Clade B = bulgaricus clade, clade D = diverse clade, Number indicates copies of gene within the genome, presence = possibility of occurrence within the clade in percent. (TXT 2464 kb)
DOI: 10.6084/m9.figshare.6181382.v1
title: Additional file 12 of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Potential HGT in Lactobacillus delbrueckii. Clade B = bulgaricus clade, clade D = diverse clade, Number indicates copies of gene within the genome, presence = possibility of occurrence within the clade in percent. (TXT 2464 kb)
DOI: 10.6084/m9.figshare.6181364
title: Additional file 8: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S6. List of structural variants identified from the genome sequencing data of 216 strains. (XLSX 2424Â kb)
DOI: 10.6084/m9.figshare.6181364.v1
title: Additional file 8: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S6. List of structural variants identified from the genome sequencing data of 216 strains. (XLSX 2424Â kb)
DOI: 10.6084/m9.figshare.6181355
title: Additional file 10: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Reconstruction of core, softcore- and pan-genome of Lactobacillus delbrueckii species with the Module algorithm of GhostKOALA. Pathways are fractured in blocks (number). Green = pathway complete; yellow = 1 block is missing in the pathway; red = 2 or more blocks are missing in the pathway. (FASTA 1473 kb)
DOI: 10.6084/m9.figshare.6181355.v1
title: Additional file 10: of Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

description: Reconstruction of core, softcore- and pan-genome of Lactobacillus delbrueckii species with the Module algorithm of GhostKOALA. Pathways are fractured in blocks (number). Green = pathway complete; yellow = 1 block is missing in the pathway; red = 2 or more blocks are missing in the pathway. (FASTA 1473 kb)
DOI: 10.6084/m9.figshare.6181346
title: Additional file 7: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S5. List of sequencing data information, assembly, and genetic distance for 216 strains in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Neurospora crassa. (XLSX 25Â kb)
DOI: 10.6084/m9.figshare.6181346.v1
title: Additional file 7: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S5. List of sequencing data information, assembly, and genetic distance for 216 strains in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Neurospora crassa. (XLSX 25Â kb)
DOI: 10.6084/m9.figshare.6181331
title: Additional file 6: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S4. Gamma parameters estimated in all pairwise comparison between Saccharomyces cerevisiae, Schizosaccharomyces pombe and Neurospora crassa and other species. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6181331.v1
title: Additional file 6: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S4. Gamma parameters estimated in all pairwise comparison between Saccharomyces cerevisiae, Schizosaccharomyces pombe and Neurospora crassa and other species. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6181274
title: Additional file 3: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S3. Raw data of gene order divergence and sequence distance. (XLSX 294Â kb)
DOI: 10.6084/m9.figshare.6181274.v1
title: Additional file 3: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S3. Raw data of gene order divergence and sequence distance. (XLSX 294Â kb)
DOI: 10.6084/m9.figshare.6181259
title: Additional file 2: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S2. List of genes in 160 orthologous groups identified in this study. (XLSX 134Â kb)
DOI: 10.6084/m9.figshare.6181259.v1
title: Additional file 2: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S2. List of genes in 160 orthologous groups identified in this study. (XLSX 134Â kb)
DOI: 10.6084/m9.figshare.6181241
title: Additional file 1: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S1. List of species examined in this study and genome assembly version. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6181241.v1
title: Additional file 1: of Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

description: Table S1. List of species examined in this study and genome assembly version. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6181151
title: SAS code from Noisy anthropogenic infrastructure interferes with alarm responses in Savannah sparrows (<i>Passerculus sandwichensis</i>)

description: statistical code used in analyzing data for this study
DOI: 10.6084/m9.figshare.6181151.v1
title: SAS code from Noisy anthropogenic infrastructure interferes with alarm responses in Savannah sparrows (<i>Passerculus sandwichensis</i>)

description: statistical code used in analyzing data for this study
DOI: 10.15131/shef.data.6181136
title: Mortgage Lending in Great Britain (link)

description: This website provides interactive mapping of outstanding residential mortgage lending by postcode sector across Great Britain, as published by individual banks, via the Council of Mortgage Lenders. This first iteration of the website - published in January 2014 - uses the most recent bank lending data, which covers the period up to the end of June 2013. I hope to update the website with future data releases, if I have the time. The map is coloured so that there are roughly the same number of areas in each category displayed in the key to the right. It's important to remember that this data release covers only seven major lenders and about three quarters of the mortgage market - it is not the full story but it does give us interesting insights that were previously not possible. The release did not include mortgage lending data for Northern Ireland, so that's why it's not included here. I've included a large interactive map on the home page and if you click below that you can see a full screen map. I've also added in some tabs which show postcode sectors in and around London, Glasgow, Manchester and Cardiff but if you want to find somewhere else you can easily pan and zoom to it via the big map.
DOI: 10.15131/shef.data.6181136.v1
title: Mortgage Lending in Great Britain (link)

description: This website provides interactive mapping of outstanding residential mortgage lending by postcode sector across Great Britain, as published by individual banks, via the Council of Mortgage Lenders. This first iteration of the website - published in January 2014 - uses the most recent bank lending data, which covers the period up to the end of June 2013. I hope to update the website with future data releases, if I have the time. The map is coloured so that there are roughly the same number of areas in each category displayed in the key to the right. It's important to remember that this data release covers only seven major lenders and about three quarters of the mortgage market - it is not the full story but it does give us interesting insights that were previously not possible. The release did not include mortgage lending data for Northern Ireland, so that's why it's not included here. I've included a large interactive map on the home page and if you click below that you can see a full screen map. I've also added in some tabs which show postcode sectors in and around London, Glasgow, Manchester and Cardiff but if you want to find somewhere else you can easily pan and zoom to it via the big map.
DOI: 10.6084/m9.figshare.6181133
title: Supplemental information 2: phylogenetic character matrix from A critical revision of the fossil record, stratigraphy and diversity of the Neogene seal genus <i>Monotherium</i> (Carnivora, Phocidae)

description: Nexus file containing the phylogenetic character matrix used in the study
DOI: 10.6084/m9.figshare.6181133.v1
title: Supplemental information 2: phylogenetic character matrix from A critical revision of the fossil record, stratigraphy and diversity of the Neogene seal genus <i>Monotherium</i> (Carnivora, Phocidae)

description: Nexus file containing the phylogenetic character matrix used in the study
DOI: 10.6084/m9.figshare.6181112
title: Data origin from Structural design of the minute clypeasteroid echinoid <i>Echinocyamus pusillus</i>

description: Table provides slice numbers from which analysis where conducted
DOI: 10.6084/m9.figshare.6181112.v1
title: Data origin from Structural design of the minute clypeasteroid echinoid <i>Echinocyamus pusillus</i>

description: Table provides slice numbers from which analysis where conducted
DOI: 10.6084/m9.figshare.6181109
title: volumetric analyses from Structural design of the minute clypeasteroid echinoid <i>Echinocyamus pusillus</i>

description: Table provides results of stereom density analuses
DOI: 10.6084/m9.figshare.6181109.v1
title: volumetric analyses from Structural design of the minute clypeasteroid echinoid <i>Echinocyamus pusillus</i>

description: Table provides results of stereom density analuses