cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/130856
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SP1819 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216415
title: Additional file 1: of Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

description: Figure S1. Time-course (24, 48, 120 and 288 h) dual growth of S. marcescens UENF-22GI with the phytopathogenic Fusarium solani on potato dextrose agar (PDA) solid medium. Note that F. solani colony growth (i.e. spread) was reduced by S. marcescens UENF-22GI, which in contrast was not significantly affected by the fungus, despite some alterations in the pigmentation patterns. At the bottom line, we show that S. marcescens UENF-22GI does not counter the growth of the beneficial saprophytic fungus Trichoderma sp.. We also observed a depigmentation of the S. marcescens UENF-22GI colony and its spread on the plate surrounding Trichoderma sp.. Finally, we used another bacteria species, Herbaspirillum seropedicae, to demonstrate that the S. marcescens UENF-22GI effects on Fusarium are not spurious or merely due to physical occupation of the Petri dish. Figure S2. General genomic features of S. marcescens UENF-22GI. a) Total length, number of protein-coding, tRNA and rRNA genes are represented, as well as the GC skew across the genome; b) BUSCO genome completeness assessment using 781 single-copy genes from the Enterobacteriales reference dataset. Figure S3. a) Maximum likelihood phylogenetic tree reconstructed with the alignments of the protein products of the 1815 core genes identified using 238 S. marcescens isolates. The tree was built with FastTree 2.1 ( https://doi.org/10.1371/journal.pone.0009490 ). Branch labels represent SH local support values. The purple shaded box delimits the clade containing S. marcescens UENF-22GI and is mostly comprised of non-clinical strains; b) Clustering analysis of S. marcescens strains using Average nucleotide identity (ANI). This analysis also supports that S. marcescens UENF-22GI belongs to a mostly non-clinical clade. Figure S4. Plant growth-promoting operons found in the S. marcescens UENF-22GI genome. a) biosynthesis of pqq; b) phosphate transport system; c) poly-beta-1,6-N-acetyl-glucosamine biosynthesis; d) bacterial cellulose biosynthesis; e) prodigiosin biosynthesis; f) type VI secretion system (genes of unknown functions are in gray). Table S1. List of genomes used in this study. Table S2. List of unique genes in the S. marcescens UENF-22GI genome. Table S3. Whole-genome similarity metrics of S. marcescens genomes used in this study. The table contains the following metrics: average nucleotide identity, average amino acid identity and digital DNA:DNA hybridization (dDDH). Table S4. Presence/absence profiles of potential plant-growth promotion genes across S. marcescens strains. Table S5. List of genes conserved in all the strains from the S. marcescens UENF-22GI and absent in the other strains used in the pan-genome analysis. (ZIP 13900 kb)
DOI: 10.6084/m9.figshare.7216415.v1
title: Additional file 1: of Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

description: Figure S1. Time-course (24, 48, 120 and 288 h) dual growth of S. marcescens UENF-22GI with the phytopathogenic Fusarium solani on potato dextrose agar (PDA) solid medium. Note that F. solani colony growth (i.e. spread) was reduced by S. marcescens UENF-22GI, which in contrast was not significantly affected by the fungus, despite some alterations in the pigmentation patterns. At the bottom line, we show that S. marcescens UENF-22GI does not counter the growth of the beneficial saprophytic fungus Trichoderma sp.. We also observed a depigmentation of the S. marcescens UENF-22GI colony and its spread on the plate surrounding Trichoderma sp.. Finally, we used another bacteria species, Herbaspirillum seropedicae, to demonstrate that the S. marcescens UENF-22GI effects on Fusarium are not spurious or merely due to physical occupation of the Petri dish. Figure S2. General genomic features of S. marcescens UENF-22GI. a) Total length, number of protein-coding, tRNA and rRNA genes are represented, as well as the GC skew across the genome; b) BUSCO genome completeness assessment using 781 single-copy genes from the Enterobacteriales reference dataset. Figure S3. a) Maximum likelihood phylogenetic tree reconstructed with the alignments of the protein products of the 1815 core genes identified using 238 S. marcescens isolates. The tree was built with FastTree 2.1 ( https://doi.org/10.1371/journal.pone.0009490 ). Branch labels represent SH local support values. The purple shaded box delimits the clade containing S. marcescens UENF-22GI and is mostly comprised of non-clinical strains; b) Clustering analysis of S. marcescens strains using Average nucleotide identity (ANI). This analysis also supports that S. marcescens UENF-22GI belongs to a mostly non-clinical clade. Figure S4. Plant growth-promoting operons found in the S. marcescens UENF-22GI genome. a) biosynthesis of pqq; b) phosphate transport system; c) poly-beta-1,6-N-acetyl-glucosamine biosynthesis; d) bacterial cellulose biosynthesis; e) prodigiosin biosynthesis; f) type VI secretion system (genes of unknown functions are in gray). Table S1. List of genomes used in this study. Table S2. List of unique genes in the S. marcescens UENF-22GI genome. Table S3. Whole-genome similarity metrics of S. marcescens genomes used in this study. The table contains the following metrics: average nucleotide identity, average amino acid identity and digital DNA:DNA hybridization (dDDH). Table S4. Presence/absence profiles of potential plant-growth promotion genes across S. marcescens strains. Table S5. List of genes conserved in all the strains from the S. marcescens UENF-22GI and absent in the other strains used in the pan-genome analysis. (ZIP 13900 kb)
DOI: 10.7284/130853
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1819 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130854
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1819 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130855
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1819 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216400
title: Additional file 1: of Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants

description: Model results. (XLSX 153 kb)
DOI: 10.6084/m9.figshare.7216400.v1
title: Additional file 1: of Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants

description: Model results. (XLSX 153 kb)
DOI: 10.6084/m9.figshare.7216391
title: Additional file 4: of Activation of a gene network in durum wheat roots exposed to cadmium

description: List of the 299 commonly up-regulated genes in roots of Creso and Svevo cvs. In this *.xlsx file are reported the expression levels of the 299 contigs that are commonly up-regulated by cadmium treatment in roots of the Creso and Svevo cvs. The first column enlists the contigs identification numbers. From column B to I are reported the mean expression values (FPKM) observed in the different genotypes, tissues and treatments. From column J to M are reported the relative annotation of each contig based on GO and TAIR databases. (XLSX 50 kb)
DOI: 10.7284/130857
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1819 using a Furuno GP-170 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216391.v1
title: Additional file 4: of Activation of a gene network in durum wheat roots exposed to cadmium

description: List of the 299 commonly up-regulated genes in roots of Creso and Svevo cvs. In this *.xlsx file are reported the expression levels of the 299 contigs that are commonly up-regulated by cadmium treatment in roots of the Creso and Svevo cvs. The first column enlists the contigs identification numbers. From column B to I are reported the mean expression values (FPKM) observed in the different genotypes, tissues and treatments. From column J to M are reported the relative annotation of each contig based on GO and TAIR databases. (XLSX 50 kb)
DOI: 10.7284/130852
title: Gyrocompass data collected during research cruise SP1819 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216376
title: Additional file 3: of Activation of a gene network in durum wheat roots exposed to cadmium

description: Level of expression (FPKM) of shoot samples of Creso and Svevo cvs. In this *.xlsx file are reported the expression levels of about 180,000 contigs in leaves of the Creso and Svevo cvs. The first column enlists the contigs identification numbers. From column B to E are reported the mean expression values (FPKM) observed in the different genotypes and treatments. (XLSX 9732 kb)
DOI: 10.7284/130851
title: Meteorological Station data collected during research cruise SP1819 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216376.v1
title: Additional file 3: of Activation of a gene network in durum wheat roots exposed to cadmium

description: Level of expression (FPKM) of shoot samples of Creso and Svevo cvs. In this *.xlsx file are reported the expression levels of about 180,000 contigs in leaves of the Creso and Svevo cvs. The first column enlists the contigs identification numbers. From column B to E are reported the mean expression values (FPKM) observed in the different genotypes and treatments. (XLSX 9732 kb)
DOI: 10.7284/130850
title: Winch data collected during research cruise SP1819 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130858
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1820 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216361
title: Additional file 2: of Activation of a gene network in durum wheat roots exposed to cadmium

description: Level of expression (FPKM) of root samples of Creso and Svevo cvs durum. In this *.xlsx file are reported the expression levels of about 180,000 contigs in roots of the Creso and Svevo cvs. The first column enlists the contigs identification numbers. From column B to E are reported the mean expression values (FPKM) observed in the different genotypes and treatments. (XLSX 9887 kb)
DOI: 10.6084/m9.figshare.7216361.v1
title: Additional file 2: of Activation of a gene network in durum wheat roots exposed to cadmium

description: Level of expression (FPKM) of root samples of Creso and Svevo cvs durum. In this *.xlsx file are reported the expression levels of about 180,000 contigs in roots of the Creso and Svevo cvs. The first column enlists the contigs identification numbers. From column B to E are reported the mean expression values (FPKM) observed in the different genotypes and treatments. (XLSX 9887 kb)
DOI: 10.7284/130862
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1820 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130863
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1820 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130864
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1820 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130866
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1820 using a Furuno GP-170 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130861
title: Gyrocompass data collected during research cruise SP1820 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130860
title: Meteorological Station data collected during research cruise SP1820 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130859
title: Winch data collected during research cruise SP1820 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130867
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1821 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130872
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1821 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130873
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1821 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216301
title: Additional file 1: of Progranulin reduces insoluble TDP-43 levels, slows down axonal degeneration and prolongs survival in mutant TDP-43 mice

description: Table S1. Results of the gene set enrichment analysis. Table S2. List of the 35 differentially expressed genes when comparing NTG controls to TDP-43(A315T) mice. Figure S1. PGRN overexpression does not affect endogenous PGRN or CTSD levels/activity. Figure S2. RNAseq results. Figure S3. Western blot of Rsad2. (A) Western blot for Rsad2 in brain and spinal cord lysates from NTG, TDP-43(A315T) and TDP-43(A315T)xGRN mice. (B) Quantification of Rsad2 bands from brain and spinal cord of NTG, TDP-43(A315T) and TDP-43(A315T)xGRN mice (n = 3 per group, * p
DOI: 10.6084/m9.figshare.7216301.v1
title: Additional file 1: of Progranulin reduces insoluble TDP-43 levels, slows down axonal degeneration and prolongs survival in mutant TDP-43 mice

description: Table S1. Results of the gene set enrichment analysis. Table S2. List of the 35 differentially expressed genes when comparing NTG controls to TDP-43(A315T) mice. Figure S1. PGRN overexpression does not affect endogenous PGRN or CTSD levels/activity. Figure S2. RNAseq results. Figure S3. Western blot of Rsad2. (A) Western blot for Rsad2 in brain and spinal cord lysates from NTG, TDP-43(A315T) and TDP-43(A315T)xGRN mice. (B) Quantification of Rsad2 bands from brain and spinal cord of NTG, TDP-43(A315T) and TDP-43(A315T)xGRN mice (n = 3 per group, * p
DOI: 10.7284/130874
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1821 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130876
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1821 using a Furuno GP-170 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216286
title: Additional file 2: of High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

description: Table S1. Comprehensive analysis with locus_tag information on virulence genes, virulence-related genes, motility, chemotaxis, iron metabolism, resistance to oxidative stress, quorum sensing related genes and regulators within analyzed P. parmentieri strains. Format: xlsx file. (XLSX 74 kb)
DOI: 10.6084/m9.figshare.7216286.v1
title: Additional file 2: of High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

description: Table S1. Comprehensive analysis with locus_tag information on virulence genes, virulence-related genes, motility, chemotaxis, iron metabolism, resistance to oxidative stress, quorum sensing related genes and regulators within analyzed P. parmentieri strains. Format: xlsx file. (XLSX 74 kb)
DOI: 10.7284/130871
title: Gyrocompass data collected during research cruise SP1821 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130870
title: Meteorological Station data collected during research cruise SP1821 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130869
title: Winch data collected during research cruise SP1821 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130877
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1822 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130882
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1822 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130883
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1822 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130884
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1822 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216244
title: Additional file 1: of Species distribution and seasonal dynamics of equine tick infestation in two Mediterranean climate niches in Israel

description: Table S1. Ticks collected at each farm and season. For each farm the geographical coordinates are specified, along with the number of horses examined for each season, the number of ticks collected of each species, and the average number of ticks per horse. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7216244.v1
title: Additional file 1: of Species distribution and seasonal dynamics of equine tick infestation in two Mediterranean climate niches in Israel

description: Table S1. Ticks collected at each farm and season. For each farm the geographical coordinates are specified, along with the number of horses examined for each season, the number of ticks collected of each species, and the average number of ticks per horse. (XLSX 16 kb)
DOI: 10.7284/130886
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1822 using a Furuno GP-170 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130881
title: Gyrocompass data collected during research cruise SP1822 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130880
title: Meteorological Station data collected during research cruise SP1822 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130879
title: Winch data collected during research cruise SP1822 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130887
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1823 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7216154
title: Chartier et al 2018 - Supplementary file - Design of microfluidic design from Whole-head recording of chemosensory activity in the marine annelid <i>Platynereis dumerilii</i>

description: .dwg file for reusing the device design
DOI: 10.6084/m9.figshare.7216154.v1
title: Chartier et al 2018 - Supplementary file - Design of microfluidic design from Whole-head recording of chemosensory activity in the marine annelid <i>Platynereis dumerilii</i>

description: .dwg file for reusing the device design
DOI: 10.6084/m9.figshare.7216151
title: Chartier et al. 2018 - Supplementary table 2 - Scoring of responses_machine-readable from Whole-head recording of chemosensory activity in the marine annelid <i>Platynereis dumerilii</i>

description: Chemical detection is key to various behaviours in both marine and terrestrial animals. Marine species, though highly diverse, have been underrepresented so far in studies on chemosensory systems, and our knowledge mostly concerns the detection of airborne cues. A broader comparative approach is therefore desirable. Marine annelid worms with their rich behavioural repertoire represent attractive models for chemosensory studies. Here, we study the marine worm <i>Platynereis dumerilii</i> to provide the first comprehensive study of head chemosensory organ physiology in an annelid. By combining microfluidics and calcium imaging, we record neuronal activity in the entire head of early juveniles upon chemical stimulation. We find that <i>Platynereis</i> uses four types of organs to detect stimuli such as alcohols, esters, amino acids and sugars. Antennae, but not nuchal organs or palps as generally hypothesized in annelids, are the main chemosensory organs. We report chemically evoked activity in possible downstream brain regions including the mushroom bodies (MBs), which are anatomically and molecularly similar to insect MBs. We conclude that chemosensation is a major sensory modality for marine annelids and propose early <i>Platynereis</i> juveniles as a model to study annelid chemosensory systems.