cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12554648
title: Supporting data of the black tiger shrimp (Penaeus monodon) genome assembly

description: The black tiger shrimp, <i>Penaeus monodon</i> (Fabricius, 1798) is a valuable commercial marine species in the inshore region of India Ocean and Southeast Asia. Even with extensive application of sequencing, genome resources are still lack in shrimp because of high heterozygosity and extremely high proportion of repeat sequences. In this study, the genome assembly of the black tiger shrimp was constructed in a hybrid strategy with Pacbio long reads and Illumna short reads. The contig N50 and scaffold N50 of the preliminary assembly were 116.8 kb and 268.5 kb, respectively. The scaffolds were anchored into chromosome-level assembly with Hi-C. The chromosome-level assembly was 2.1 Gb, accounting for 90.2% of the estimated genome size, and consisted of 53.7% of repeat sequences. A total of 29,387 protein-coding genes were predicted, 75.6% of which were successfully annotated with putative function. Furthermore, divergence between the black tiger shrimp and Pacific white shrimp was estimated to be 2.79 million years ago. And the population size of black tiger shrimp had been increasing since 50,000 years ago. This assembly is the second chromosome-level assembly in shrimp, and will be a valuable genomic resource for conservation and breeding studies of the black tiger shrimp in the future research.
DOI: 10.6084/m9.figshare.6616775
title: Additional file 1: of iTRAQ-Based Proteomic Analysis reveals possible target-related proteins and signal networks in human osteoblasts overexpressing FGFR2

description: Figure S1. Overview of iTRAQ data analysis. (A) The basic statistics of the iTRAQ data. (B) Peptide length distribution. X-axis showed the peptide length, while Y-axis showed the corresponding peptide count. (C) Molecular weight distribution of the identified proteins. X-axis showed molecular weight (kDa), while y-axis showed number of proteins. Table S1. Protein list identified in biological replicate 1 and 2 with an FDR of 0.01% at the peptide level. Table S2. The categories enriched molecular function (MF) by GO annotation. Table S3. The categories enriched biological process (BP) by GO annotation. Table S4. The categories enriched cellular component (CC) by GO annotation. Figure S2. Real time PCR analyses of TNNI3 and UBE2E3 in hFOB cells overexpressing FGFR2 and control cells. Statistics analysis were performed using non-paired Studentâ s t-test, with *** representing p &lt; 0.01. (ZIP 606 kb)
DOI: 10.6084/m9.figshare.6616775.v1
title: Additional file 1: of iTRAQ-Based Proteomic Analysis reveals possible target-related proteins and signal networks in human osteoblasts overexpressing FGFR2

description: Figure S1. Overview of iTRAQ data analysis. (A) The basic statistics of the iTRAQ data. (B) Peptide length distribution. X-axis showed the peptide length, while Y-axis showed the corresponding peptide count. (C) Molecular weight distribution of the identified proteins. X-axis showed molecular weight (kDa), while y-axis showed number of proteins. Table S1. Protein list identified in biological replicate 1 and 2 with an FDR of 0.01% at the peptide level. Table S2. The categories enriched molecular function (MF) by GO annotation. Table S3. The categories enriched biological process (BP) by GO annotation. Table S4. The categories enriched cellular component (CC) by GO annotation. Figure S2. Real time PCR analyses of TNNI3 and UBE2E3 in hFOB cells overexpressing FGFR2 and control cells. Statistics analysis were performed using non-paired Studentâ s t-test, with *** representing p &lt; 0.01. (ZIP 606 kb)
DOI: 10.6084/m9.figshare.6616571
title: MOESM7 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

description: Additional file 7. Genomic loci of the analyzed Bathyarchaeota MAGs encoding those enzymatic functions, which are mentioned in the metabolic scheme (Fig.Â 3) as well as in the main text. n.d., not determined.
DOI: 10.6084/m9.figshare.6616571.v1
title: MOESM7 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

description: Additional file 7. Genomic loci of the analyzed Bathyarchaeota MAGs encoding those enzymatic functions, which are mentioned in the metabolic scheme (Fig.Â 3) as well as in the main text. n.d., not determined.
DOI: 10.6084/m9.figshare.6616547
title: Additional file 1: of Species composition and habitat preferences of the nearshore fish fauna of Bonne Bay, Newfoundland

description: Photographs. Views of the dorsal (photo 1) and ventral (photo 2) surfaces of an immature male winter skate (Leucoraja ocellata) collected from Bonne Bay on 7 July 2010. The dorsal surface has three or more rows of thorns forming an arrow pattern along the centre of the back (Nozères et al. 2010). The length of this specimen (54 cm) and size of its claspers indicate this specimen is the late-maturing type, an adaptation to coastal waters of western Newfoundland (Gauthier and Nozères 2016). (ZIP 133 kb)
DOI: 10.6084/m9.figshare.6616547.v1
title: Additional file 1: of Species composition and habitat preferences of the nearshore fish fauna of Bonne Bay, Newfoundland

description: Photographs. Views of the dorsal (photo 1) and ventral (photo 2) surfaces of an immature male winter skate (Leucoraja ocellata) collected from Bonne Bay on 7 July 2010. The dorsal surface has three or more rows of thorns forming an arrow pattern along the centre of the back (Nozères et al. 2010). The length of this specimen (54 cm) and size of its claspers indicate this specimen is the late-maturing type, an adaptation to coastal waters of western Newfoundland (Gauthier and Nozères 2016). (ZIP 133 kb)
DOI: 10.6084/m9.figshare.6616517
title: MOESM4 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

description: Additional file 4. Compiled metagenome-assembled genomes that met the criteria of a minimum of 50% genome completeness and contamination rates of 10%.
DOI: 10.6084/m9.figshare.6616517.v1
title: MOESM4 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

description: Additional file 4. Compiled metagenome-assembled genomes that met the criteria of a minimum of 50% genome completeness and contamination rates of 10%.
DOI: 10.6084/m9.figshare.6616505
title: Additional file 2: of Identification of five novel genetic loci related to facial morphology by genome-wide association studies

description: Table S2. Correlations of face traits. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.6616505.v1
title: Additional file 2: of Identification of five novel genetic loci related to facial morphology by genome-wide association studies

description: Table S2. Correlations of face traits. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.6616496
title: MOESM3 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

description: Additional file 3. Sequencing and assembly statistics of the metagenome data for the microbial communities of the thermophilic and mesophilic biogas reactor systems. UASS, upflow anaerobic solid-state reactor; AF, anaerobic filter; n.d., not determined.
DOI: 10.6084/m9.figshare.6616496.v1
title: MOESM3 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

description: Additional file 3. Sequencing and assembly statistics of the metagenome data for the microbial communities of the thermophilic and mesophilic biogas reactor systems. UASS, upflow anaerobic solid-state reactor; AF, anaerobic filter; n.d., not determined.
DOI: 10.6084/m9.figshare.6616484
title: Additional file 1: of Identification of five novel genetic loci related to facial morphology by genome-wide association studies

description: Table S1. Correlation between face traits and covariates. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6616484.v1
title: Additional file 1: of Identification of five novel genetic loci related to facial morphology by genome-wide association studies

description: Table S1. Correlation between face traits and covariates. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6616472
title: MOESM2 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

description: Additional file 2. Previously published MAGs for the phylum Bathyarchaeota. The phylogenetic affiliation is shown in Fig.Â 2. *, completeness and contamination were estimated by CheckM [25].
DOI: 10.6084/m9.figshare.6616472.v1
title: MOESM2 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

description: Additional file 2. Previously published MAGs for the phylum Bathyarchaeota. The phylogenetic affiliation is shown in Fig.Â 2. *, completeness and contamination were estimated by CheckM [25].
DOI: 10.6084/m9.figshare.6616424
title: Additional file 2: of Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

description: Figure S1. Phylogenetic tree of mtDNA macrohaplogroup L complete African sequences produced in this study. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.6616424.v1
title: Additional file 2: of Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

description: Figure S1. Phylogenetic tree of mtDNA macrohaplogroup L complete African sequences produced in this study. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.6616409
title: Additional file 1: of Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

description: Table S1. Complete mtDNA macrohaplogroup L sequences. Table S2. Frequencies of mtDNA haplogroups L2 and L3 and Y-chromosome haplogroup E lineages across Africa. Table S3. Coalescence ages in thousand years (kya) with 95% coefficient intervals (CI), or standard deviations, for the main mitochondrial DNA African haplogroups. Table S4. Coalescence ages in thousand years (kya) with 95% coefficient intervals (CI), or standard deviations, for Y-chromosome most recent common ancestor (MRCA), the out-of-Africa event, and the splits of haplogroup DE and E. Table S5. Population clustering into five classes. Table S6. k-means cluster results using African populations characterized by mtDNA L3 and Y-chromosome E haplogroup frequencies. Table S7. k-means cluster results using African populations characterized by mtDNA L2 and L3 and Y-chromosome E haplogroup frequencies. (XLSX 403 kb)
DOI: 10.6084/m9.figshare.6616409.v1
title: Additional file 1: of Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

description: Table S1. Complete mtDNA macrohaplogroup L sequences. Table S2. Frequencies of mtDNA haplogroups L2 and L3 and Y-chromosome haplogroup E lineages across Africa. Table S3. Coalescence ages in thousand years (kya) with 95% coefficient intervals (CI), or standard deviations, for the main mitochondrial DNA African haplogroups. Table S4. Coalescence ages in thousand years (kya) with 95% coefficient intervals (CI), or standard deviations, for Y-chromosome most recent common ancestor (MRCA), the out-of-Africa event, and the splits of haplogroup DE and E. Table S5. Population clustering into five classes. Table S6. k-means cluster results using African populations characterized by mtDNA L3 and Y-chromosome E haplogroup frequencies. Table S7. k-means cluster results using African populations characterized by mtDNA L2 and L3 and Y-chromosome E haplogroup frequencies. (XLSX 403 kb)
DOI: 10.6084/m9.figshare.6616403
title: Additional file 9: of Absolute quantitation of microbiota abundance in environmental samples

description: Modified Bash code including Unoise3 command. (XLSX 422 kb)
DOI: 10.6084/m9.figshare.6616403.v1
title: Additional file 9: of Absolute quantitation of microbiota abundance in environmental samples

description: Modified Bash code including Unoise3 command. (XLSX 422 kb)
DOI: 10.6084/m9.figshare.6616397
title: Additional file 12: of Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC

description: Data, metadata files, and R scripts used to generate the figures. The Rmarkdown_data_metadata.zip is a compressed folder containing the Rmarkdown file, which details the analysis scripts (in both RMD and HTML format). The batch file used to process the sequence data in mothur is provided. Microbiome data is included here as a BIOM-formatted table. All other data (metabolomics and cytokine expression) along with metadata are CSV files. (ZIP 992Â kb)
DOI: 10.6084/m9.figshare.6616397.v1
title: Additional file 12: of Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC

description: Data, metadata files, and R scripts used to generate the figures. The Rmarkdown_data_metadata.zip is a compressed folder containing the Rmarkdown file, which details the analysis scripts (in both RMD and HTML format). The batch file used to process the sequence data in mothur is provided. Microbiome data is included here as a BIOM-formatted table. All other data (metabolomics and cytokine expression) along with metadata are CSV files. (ZIP 992Â kb)
DOI: 10.6084/m9.figshare.6616391
title: Additional file 2: of Anchored phylogenomics illuminates the skipper butterfly tree of life

description: Table presenting detailed information of the AHE matrix composition, including locus information, capture rate, probe region length, GC content and parsimony informative Sites. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.6616391.v1
title: Additional file 2: of Anchored phylogenomics illuminates the skipper butterfly tree of life

description: Table presenting detailed information of the AHE matrix composition, including locus information, capture rate, probe region length, GC content and parsimony informative Sites. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.6616382
title: Additional file 8: of Absolute quantitation of microbiota abundance in environmental samples

description: Bash code for the sequencing analysis. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.6616382.v1
title: Additional file 8: of Absolute quantitation of microbiota abundance in environmental samples

description: Bash code for the sequencing analysis. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.6616370
title: Additional file 1: of Anchored phylogenomics illuminates the skipper butterfly tree of life

description: Table of taxon sampling presenting detailed information for each specimen used in this study, along with number of captured AHE loci and genetic coverage in the AHE dataset. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6616370.v1
title: Additional file 1: of Anchored phylogenomics illuminates the skipper butterfly tree of life

description: Table of taxon sampling presenting detailed information for each specimen used in this study, along with number of captured AHE loci and genetic coverage in the AHE dataset. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6616367
title: Additional file 4: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

description: Scripts and combined dataset to analyse the presence of hemoparasites in Psittaciformes. Analyses and the combined dataset for the effects of diet, habitat, climate, screening method (as factors) and species (as a random variable) on the presence of parasites in the studied individuals using a binomial General Lineal Mixed-Effects Model and model averaging based on Akaike information criterion (AIC) with R. Scripts for the 10-fold cross validation and the calculations of parasite detection probability are also provided. (TXT 34 kb)
DOI: 10.6084/m9.figshare.6616367.v1
title: Additional file 4: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

description: Scripts and combined dataset to analyse the presence of hemoparasites in Psittaciformes. Analyses and the combined dataset for the effects of diet, habitat, climate, screening method (as factors) and species (as a random variable) on the presence of parasites in the studied individuals using a binomial General Lineal Mixed-Effects Model and model averaging based on Akaike information criterion (AIC) with R. Scripts for the 10-fold cross validation and the calculations of parasite detection probability are also provided. (TXT 34 kb)
DOI: 10.6084/m9.figshare.6616358
title: Additional file 7: of Absolute quantitation of microbiota abundance in environmental samples

description: Description of samples submitted to EBI server. (XLSX 74 kb)
DOI: 10.6084/m9.figshare.6616358.v1
title: Additional file 7: of Absolute quantitation of microbiota abundance in environmental samples

description: Description of samples submitted to EBI server. (XLSX 74 kb)
DOI: 10.6084/m9.figshare.6616349
title: Additional file 6: of Absolute quantitation of microbiota abundance in environmental samples

description: qPCR data. (TXT 12 kb)
DOI: 10.6084/m9.figshare.6616349.v1
title: Additional file 6: of Absolute quantitation of microbiota abundance in environmental samples

description: qPCR data. (TXT 12 kb)
DOI: 10.6084/m9.figshare.6616346
title: Additional file 3: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

description: Table S2. Main food items consumed by the Psittaciformes species in the localities where the blood parasite sampling was carried out. Details on the species, main food items and parts consumed are provided. The presence of secondary metabolites with antimalarial/general antiparasitic plant secondary metabolites, anthelmintic, antimicrobial, and antioxidant properties is indicated. Source references are provided. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.6616346.v1
title: Additional file 3: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

description: Table S2. Main food items consumed by the Psittaciformes species in the localities where the blood parasite sampling was carried out. Details on the species, main food items and parts consumed are provided. The presence of secondary metabolites with antimalarial/general antiparasitic plant secondary metabolites, anthelmintic, antimicrobial, and antioxidant properties is indicated. Source references are provided. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.6616307
title: Additional file 4: of Absolute quantitation of microbiota abundance in environmental samples

description: Figure S1. Model of synthetic spike addition. Number of sequencing reads of synthetic spike per 1000 total reads (y axis) from 16 s rRNA, 18S rRNA and ITS following addition to soil of different levels of P, E and F synthetic spikes (x axis). The figure presents the full dataset from the averaged dataset shown on Fig. 3. (TXT 39 kb)
DOI: 10.6084/m9.figshare.6616307.v1
title: Additional file 4: of Absolute quantitation of microbiota abundance in environmental samples

description: Figure S1. Model of synthetic spike addition. Number of sequencing reads of synthetic spike per 1000 total reads (y axis) from 16 s rRNA, 18S rRNA and ITS following addition to soil of different levels of P, E and F synthetic spikes (x axis). The figure presents the full dataset from the averaged dataset shown on Fig. 3. (TXT 39 kb)
DOI: 10.6084/m9.figshare.6616295
title: Additional file 1: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

description: Table S1. Hemoparasites in wild Psittaciformes. Malaria parasites (Plasmodium), related intracellular haemosporidians (Haemoproteus and Leucocytozoon), the unicellular parasitic flagellate protozoans (Trypanosoma), and microfilaria reported in wild populations of Psittaciformes. The probability of detection for adults is based on a simulation (see Additional file 4) of the probability that the parasites will actually be detected given the sample size and an expected true prevalence based on the prevalences observed in wild Psittaciformes. The habitat and climate classification follow the references in Table 1. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6616295.v1
title: Additional file 1: of Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

description: Table S1. Hemoparasites in wild Psittaciformes. Malaria parasites (Plasmodium), related intracellular haemosporidians (Haemoproteus and Leucocytozoon), the unicellular parasitic flagellate protozoans (Trypanosoma), and microfilaria reported in wild populations of Psittaciformes. The probability of detection for adults is based on a simulation (see Additional file 4) of the probability that the parasites will actually be detected given the sample size and an expected true prevalence based on the prevalences observed in wild Psittaciformes. The habitat and climate classification follow the references in Table 1. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6616286
title: Additional file 3: of Absolute quantitation of microbiota abundance in environmental samples

description: Data used for figures and tables preparation. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6616286.v1
title: Additional file 3: of Absolute quantitation of microbiota abundance in environmental samples

description: Data used for figures and tables preparation. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6616259
title: Additional file 1: of Role of miR-146a in neural stem cell differentiation and neural lineage determination: relevance for neurodevelopmental disorders

description: Table S1. Detailed information of all patients and controls whose brain samples were used in this study. Table S2. Possibly deleterious variants in known ASD and ID genes. Table S3. DEGs identified in undifferentiated cells. Table S4. DEGs identified in differentiated cells. Table S5. Validation of RNA-Seq using RT-qPCR on Fluidigm array. Table S6. Top 20 cannonical pathways deregulated in undifferentiated cells. Table S7. Top 4 nodes enriched for protein-protein interaction as calculated by ClusterOne Plugin. Table S8. Top 20 cannonical pathways deregulated in the cell cycle modules of differentiated cells. Table S9. Top 20 cannonical pathways deregulated in the cell neuronal modules of differentiated cells. Table S10. Cell type enrichment analysis of DEGs from the Cell Cycle and Neuronal Modules. (XLSX 888 kb)
DOI: 10.6084/m9.figshare.6616259.v1
title: Additional file 1: of Role of miR-146a in neural stem cell differentiation and neural lineage determination: relevance for neurodevelopmental disorders

description: Table S1. Detailed information of all patients and controls whose brain samples were used in this study. Table S2. Possibly deleterious variants in known ASD and ID genes. Table S3. DEGs identified in undifferentiated cells. Table S4. DEGs identified in differentiated cells. Table S5. Validation of RNA-Seq using RT-qPCR on Fluidigm array. Table S6. Top 20 cannonical pathways deregulated in undifferentiated cells. Table S7. Top 4 nodes enriched for protein-protein interaction as calculated by ClusterOne Plugin. Table S8. Top 20 cannonical pathways deregulated in the cell cycle modules of differentiated cells. Table S9. Top 20 cannonical pathways deregulated in the cell neuronal modules of differentiated cells. Table S10. Cell type enrichment analysis of DEGs from the Cell Cycle and Neuronal Modules. (XLSX 888 kb)