cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6003884.v1
title: Additional file 12: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Microbial-assigned transcripts, full results table, annotation and DESeq2 analysis. Description of File: The table includes information on expressed microbial transcripts. 1) Phylogenetic annotation of each transcript; 2) Whether significantly expressed in root acid bog soil (RA), root limestone soil (RL), shoot acid bog soil (SA) and/or shoot limestone soil (SL). Significantly expressed transcripts is defined as the number of microbial annotated transcripts that obtained ≥5 aligned reads in at least 3 samples in each of the treatments RA (total 8 samples), RL (total 9 samples), SA (total 10 samples), SL (total 9 samples); 3) two columns indicating whether the transcript is “upregulated in acid or limestone ecotype in acid bog soil” and/or “upregulated in acid or limestone ecotype in limestone soil” 4) KOG functional annotation (KOG ID, KOG definition, KOG class, KOG group) and best BLAST match (sequence length, database that contained the best match, accession number, gene description, best match organism, e-value, percentage ID, BLAST score, percentage sequence coverage); 5) The full DESeq2 result for each pairwise comparison in shoot (list 1-4) and root (list 5-8): these columns contain the log2foldchange and adjusted P value (FDR) for pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype), shoots and roots (Shoot, Root), see sheet “DESeq2 pairwise comparisons” for further explanation of the 8 pairwise comparisons; 6) The count table. (XLSX 6498 kb)
DOI: 10.6084/m9.figshare.6003869
title: Additional file 11: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Selected fungal annotated transcript results, including those discussed in the text. The table contains the following information for selected microbial assigned transcripts that are expressed in Holcus lanatus roots, many of which discussed in the text: 1) Transcript ID; 2) Best BLAST match (taxonomic division, genus and gene description); 3) KOG annotations (KOG ID, KOG group, KOG class, KOG definition); 4) possible role; 5) relevant reference (citations for relevant references are contained in Additional file 7); 6) two columns to indicate whether the transcript was significantly upregulated in acid or limestone soil, acid or limestone ecotype; 7) The full DESeq2 result for each root pairwise comparison: these columns contain the log2foldchange and adjusted P value (FDR) for root pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype): Root Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Root Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Root Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Root La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.6003869.v1
title: Additional file 11: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

description: Selected fungal annotated transcript results, including those discussed in the text. The table contains the following information for selected microbial assigned transcripts that are expressed in Holcus lanatus roots, many of which discussed in the text: 1) Transcript ID; 2) Best BLAST match (taxonomic division, genus and gene description); 3) KOG annotations (KOG ID, KOG group, KOG class, KOG definition); 4) possible role; 5) relevant reference (citations for relevant references are contained in Additional file 7); 6) two columns to indicate whether the transcript was significantly upregulated in acid or limestone soil, acid or limestone ecotype; 7) The full DESeq2 result for each root pairwise comparison: these columns contain the log2foldchange and adjusted P value (FDR) for root pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype): Root Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Root Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Root Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Root La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.6003857
title: Additional file 1: of Ticks are more suitable than red foxes for monitoring zoonotic tick-borne pathogens in northeastern Italy

description: Table S1. Ticks collected in 2011â 2016 organized in pools, data of sites and results of molecular screening. (XLS 172 kb)
DOI: 10.6084/m9.figshare.6003857.v1
title: Additional file 1: of Ticks are more suitable than red foxes for monitoring zoonotic tick-borne pathogens in northeastern Italy

description: Table S1. Ticks collected in 2011â 2016 organized in pools, data of sites and results of molecular screening. (XLS 172 kb)
DOI: 10.6084/m9.figshare.6003827
title: Additional file 2: of Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

description: An alignment file of Alu subfamily consensus sequences. (FAS 114Â kb)
DOI: 10.6084/m9.figshare.6003827.v1
title: Additional file 2: of Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

description: An alignment file of Alu subfamily consensus sequences. (FAS 114Â kb)
DOI: 10.6084/m9.figshare.6003821
title: Additional file 1: of The mosquito holobiont: fresh insight into mosquito-microbiota interactions

description: List of bacteria, fungi and viruses found in different larva and adult mosquito species [15, 17, 18, 20–22, 24, 25, 27, 29, 32, 35–38, 52, 54, 61, 68, 69, 81, 103, 154–157]. List of articles mentioned are published since 2013. Previous publications on this research topic are available in our previous review [16]. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.6003821.v1
title: Additional file 1: of The mosquito holobiont: fresh insight into mosquito-microbiota interactions

description: List of bacteria, fungi and viruses found in different larva and adult mosquito species [15, 17, 18, 20–22, 24, 25, 27, 29, 32, 35–38, 52, 54, 61, 68, 69, 81, 103, 154–157]. List of articles mentioned are published since 2013. Previous publications on this research topic are available in our previous review [16]. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.6003809
title: Additional file 4: of Paramutation-like features of multiple natural epialleles in tomato

description: DMRs shared between introgression lines and hypomethylated in all cytosine contexts. Average proportion of methylated cytosines between two replicates, for each context and genotype. Tsv format. (TXT 1 kb)
DOI: 10.6084/m9.figshare.6003809.v1
title: Additional file 4: of Paramutation-like features of multiple natural epialleles in tomato

description: DMRs shared between introgression lines and hypomethylated in all cytosine contexts. Average proportion of methylated cytosines between two replicates, for each context and genotype. Tsv format. (TXT 1 kb)
DOI: 10.6084/m9.figshare.6003806
title: Additional file 1: of Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

description: An excel file containing different worksheets for DNA samples and PCR format, PCR primers and genomic locations of amplified insertions, subfamily counts, and genotype data with allele frequency for each locus. (XLSX 78Â kb)
DOI: 10.6084/m9.figshare.6003806.v1
title: Additional file 1: of Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

description: An excel file containing different worksheets for DNA samples and PCR format, PCR primers and genomic locations of amplified insertions, subfamily counts, and genotype data with allele frequency for each locus. (XLSX 78Â kb)
DOI: 10.6084/m9.figshare.6003794
title: Additional file 3: of Paramutation-like features of multiple natural epialleles in tomato

description: DMRs shared between introgression lines and hypermethylated in all cytosine contexts. Average proportion of methylated cytosines between two replicates, for each context and genotype. Tsv format. (TXT 4 kb)
DOI: 10.6084/m9.figshare.6003794.v1
title: Additional file 3: of Paramutation-like features of multiple natural epialleles in tomato

description: DMRs shared between introgression lines and hypermethylated in all cytosine contexts. Average proportion of methylated cytosines between two replicates, for each context and genotype. Tsv format. (TXT 4 kb)
DOI: 10.6084/m9.figshare.6003776
title: Additional file 2: of Paramutation-like features of multiple natural epialleles in tomato

description: DMRs shared between introgression lines. Tsv format. (TXT 453 kb)
DOI: 10.6084/m9.figshare.6003776.v1
title: Additional file 2: of Paramutation-like features of multiple natural epialleles in tomato

description: DMRs shared between introgression lines. Tsv format. (TXT 453 kb)
DOI: 10.6084/m9.figshare.6003764
title: Additional file 2 of SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data

description: Rat pathways from KEGG [19]. (TXT 19558 kb)
DOI: 10.6084/m9.figshare.6003764.v1
title: Additional file 2 of SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data

description: Rat pathways from KEGG [19]. (TXT 19558 kb)
DOI: 10.6084/m9.figshare.6003749
title: Additional file 1: of Paramutation-like features of multiple natural epialleles in tomato

description: Summary of MethylC-seq data. Tsv format. (TXT 358 bytes)
DOI: 10.6084/m9.figshare.6003749.v1
title: Additional file 1: of Paramutation-like features of multiple natural epialleles in tomato

description: Summary of MethylC-seq data. Tsv format. (TXT 358 bytes)
DOI: 10.6084/m9.figshare.6003746
title: Additional file 1 of SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data

description: Human pathways from PathwayAPI [18]. (TXT 2877 kb)
DOI: 10.6084/m9.figshare.6003746.v1
title: Additional file 1 of SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data

description: Human pathways from PathwayAPI [18]. (TXT 2877 kb)
DOI: 10.6084/m9.figshare.6003743
title: Additional file 5 of The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

description: GO and pathway enrichment analysis of contigs. The contigs were tested for any GO and pathway enrichment. The list of significantly enriched GOs are shown in (a). The list of significantly enriched pathways are shown in (b). (XLS 16 kb)
DOI: 10.6084/m9.figshare.6003743.v1
title: Additional file 5 of The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

description: GO and pathway enrichment analysis of contigs. The contigs were tested for any GO and pathway enrichment. The list of significantly enriched GOs are shown in (a). The list of significantly enriched pathways are shown in (b). (XLS 16 kb)
DOI: 10.6084/m9.figshare.6003734
title: Additional file 4 of The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

description: Gene expression of assembled contigs. The expression levels and expression profiles of 26,461 contigs are shown. Also, the significance level of differential expression between G3 and G5 samples are provided. (XLS 2250 kb)
DOI: 10.6084/m9.figshare.6003734.v1
title: Additional file 4 of The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

description: Gene expression of assembled contigs. The expression levels and expression profiles of 26,461 contigs are shown. Also, the significance level of differential expression between G3 and G5 samples are provided. (XLS 2250 kb)
DOI: 10.6084/m9.figshare.6003731
title: Additional file 11: of Paramutation-like features of multiple natural epialleles in tomato

description: H06 sequences for S. lycopersicum cv. M82, S. pimpinellifolium and S. pennellii LA0716. Fasta format. (FASTA 1 kb)
DOI: 10.6084/m9.figshare.6003731.v1
title: Additional file 11: of Paramutation-like features of multiple natural epialleles in tomato

description: H06 sequences for S. lycopersicum cv. M82, S. pimpinellifolium and S. pennellii LA0716. Fasta format. (FASTA 1 kb)
DOI: 10.6084/m9.figshare.6003719
title: Additional file 3 of The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

description: Annotation of assembled contigs. The list of 26,461 contigs with significant E-value using BlastX are shown. The NR and UniRef90 protein sequence databases are used for the contig search. (XLS 3270 kb)
DOI: 10.6084/m9.figshare.6003719.v1
title: Additional file 3 of The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

description: Annotation of assembled contigs. The list of 26,461 contigs with significant E-value using BlastX are shown. The NR and UniRef90 protein sequence databases are used for the contig search. (XLS 3270 kb)
DOI: 10.6084/m9.figshare.6003713
title: Additional file 5 of Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

description: Molecular and cellular functions affected by P supply (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6003713.v1
title: Additional file 5 of Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

description: Molecular and cellular functions affected by P supply (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6003710
title: Additional file 10: of Paramutation-like features of multiple natural epialleles in tomato

description: Oligonucleotides used in this study. Tsv format. (TXT 1 kb)
DOI: 10.6084/m9.figshare.6003710.v1
title: Additional file 10: of Paramutation-like features of multiple natural epialleles in tomato

description: Oligonucleotides used in this study. Tsv format. (TXT 1 kb)
DOI: 10.6084/m9.figshare.6003707
title: Additional file 8: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

description: Table S4. HHV-6 Peptides Identified by Shotgun Proteomics. Mass spectrometry database search results are shown for HHV6 peptides identified using Protein Prospector v 5.19.1 described in Materials and Methods. The table reports the best matched peptide spectra. Provided are the mass to charge ratio (m/z), charge (z), mass error in ppm, the peptide sequence with previous and next amino acids in the sequence, variable modification, the fraction and retention time as spectrum identifiers. The start and end sequence numbers are given, along with Protein Prospector peptide score and peptide expectation value. (XLSX 88Â kb)
DOI: 10.6084/m9.figshare.6003707.v1
title: Additional file 8: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

description: Table S4. HHV-6 Peptides Identified by Shotgun Proteomics. Mass spectrometry database search results are shown for HHV6 peptides identified using Protein Prospector v 5.19.1 described in Materials and Methods. The table reports the best matched peptide spectra. Provided are the mass to charge ratio (m/z), charge (z), mass error in ppm, the peptide sequence with previous and next amino acids in the sequence, variable modification, the fraction and retention time as spectrum identifiers. The start and end sequence numbers are given, along with Protein Prospector peptide score and peptide expectation value. (XLSX 88Â kb)
DOI: 10.6084/m9.figshare.6003704
title: Additional file 1: of Molecular survey of neglected bacterial pathogens reveals an abundant diversity of species and genotypes in ticks collected from animal hosts across Romania

description: Table S1. Tick-borne bacteria in Romanian ticks; details regarding tick species, locality, county, year, host, life stage of ticks and pathogen. (XLS 17 kb)
DOI: 10.6084/m9.figshare.6003704.v1
title: Additional file 1: of Molecular survey of neglected bacterial pathogens reveals an abundant diversity of species and genotypes in ticks collected from animal hosts across Romania

description: Table S1. Tick-borne bacteria in Romanian ticks; details regarding tick species, locality, county, year, host, life stage of ticks and pathogen. (XLS 17 kb)
DOI: 10.6084/m9.figshare.6003692
title: Additional file 7: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

description: Table S3. HHV-6 Proteins Identified by Shotgun Proteomics. Mass spectrometry database search results are shown for HHV6 proteins identified using Protein Prospector v 5.19.1 as described in Methods. Data were scored at the 5% FDR with Protein and Peptide minimum scores of 22 and 15, and maximum expectation values for proteins and peptides of 0.01 and 0.001, respectively. The number of unique peptides, the peptide (or spectral) count, the percent sequence coverage and the best peptide expectation value are given for each protein identification, merged from all samples. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.6003692.v1
title: Additional file 7: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

description: Table S3. HHV-6 Proteins Identified by Shotgun Proteomics. Mass spectrometry database search results are shown for HHV6 proteins identified using Protein Prospector v 5.19.1 as described in Methods. Data were scored at the 5% FDR with Protein and Peptide minimum scores of 22 and 15, and maximum expectation values for proteins and peptides of 0.01 and 0.001, respectively. The number of unique peptides, the peptide (or spectral) count, the percent sequence coverage and the best peptide expectation value are given for each protein identification, merged from all samples. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.6003689
title: Additional file 1 of The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

description: The list of SRA samples used for contig assembly. (XLS 18 kb)
DOI: 10.6084/m9.figshare.6003689.v1
title: Additional file 1 of The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature

description: The list of SRA samples used for contig assembly. (XLS 18 kb)
DOI: 10.6084/m9.figshare.6003686
title: Additional file 3 of Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

description: Probe-sets showing significantly altered mRNA abundances (per diet and tissue). The Venn diagram depicting the number of probe-sets differentially expressed in a) colon, b) jejunum, and c) kidney. Number of up-regulated probe-sets is shown in red. Number of down-regulated probe-sets is shown in green. L – Low P supply; M – Medium P supply; H – High P supply (XLSX 254 kb)
DOI: 10.6084/m9.figshare.6003686.v1
title: Additional file 3 of Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

description: Probe-sets showing significantly altered mRNA abundances (per diet and tissue). The Venn diagram depicting the number of probe-sets differentially expressed in a) colon, b) jejunum, and c) kidney. Number of up-regulated probe-sets is shown in red. Number of down-regulated probe-sets is shown in green. L – Low P supply; M – Medium P supply; H – High P supply (XLSX 254 kb)
DOI: 10.6084/m9.figshare.6003680
title: Additional file 6: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

description: Table S2. RPKM values for RNA-Seq data. (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.6003680.v1
title: Additional file 6: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

description: Table S2. RPKM values for RNA-Seq data. (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.6003671
title: Additional file 2 of Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

description: Primer used for verification of microarray by qRT-PCR (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6003671.v1
title: Additional file 2 of Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

description: Primer used for verification of microarray by qRT-PCR (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6003653
title: Additional file 1 of Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

description: Composition of the experimental diets (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6003653.v1
title: Additional file 1 of Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

description: Composition of the experimental diets (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6003635
title: MOESM4 of Seasonal change in sexual differences in nestling size and survival: a framework to evaluate sex-dependent environmental sensitivity in the wild

description: Additional file 4: Table S4. Model ranking of the GLMM for fledgling sex ratio according to the AIC.
DOI: 10.6084/m9.figshare.6003635.v1
title: MOESM4 of Seasonal change in sexual differences in nestling size and survival: a framework to evaluate sex-dependent environmental sensitivity in the wild

description: Additional file 4: Table S4. Model ranking of the GLMM for fledgling sex ratio according to the AIC.
DOI: 10.6084/m9.figshare.6003629
title: Additional file 3: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

description: Figure S2. Phylogenetic tree of HHV-6B complete U90/91 and U94/100 loci. HHV-6B genomes were aligned using MAFFT, curated for sequence outside of repeat regions, and phylogenetic trees were constructed using MrBayes along the 6 kb U90/91 (A), and 10 kb U94-100 (B) regions. HHV6-6B NY310 was used as an outgroup. Samples are colored and labeled for origin based on New York (green), Japan (blue), or iciHHV6-B from HSCT recipients or their donors in Seattle (black), as well as whether two genomes were recovered from first-degree relatives (red). Location images purchased from Adobe Stock. (ZIP 656 kb)
DOI: 10.6084/m9.figshare.6003629.v1
title: Additional file 3: of Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6

description: Figure S2. Phylogenetic tree of HHV-6B complete U90/91 and U94/100 loci. HHV-6B genomes were aligned using MAFFT, curated for sequence outside of repeat regions, and phylogenetic trees were constructed using MrBayes along the 6 kb U90/91 (A), and 10 kb U94-100 (B) regions. HHV6-6B NY310 was used as an outgroup. Samples are colored and labeled for origin based on New York (green), Japan (blue), or iciHHV6-B from HSCT recipients or their donors in Seattle (black), as well as whether two genomes were recovered from first-degree relatives (red). Location images purchased from Adobe Stock. (ZIP 656 kb)
DOI: 10.6084/m9.figshare.6003623
title: MOESM3 of Seasonal change in sexual differences in nestling size and survival: a framework to evaluate sex-dependent environmental sensitivity in the wild

description: Additional file 3: Table S3. Model ranking of the LMM for nestling wing length according to the AIC.