cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3642578_d4.v1
title: Additional file 9: Table S5. of Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

description: The statistical analysis of each group of the NJ phylogenetic tree. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3642578_d5.v1
title: Additional file 5: Table S4. of Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

description: Synonymous and non-synonymous substitution rates and the estimated times for the tandem and segmental duplication events in GhMYB genes. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3642578_d6.v1
title: Additional file 10: Table S6. of Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

description: The Ka/Ks ratios of MYB gene family in cotton (Gcpb raimodii/upland cotton). (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3642578_d8.v1
title: Additional file 2: Table S2. of Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

description: Classification of MYB genes according to MYB repeat domains and protein length. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3642578_d9.v1
title: Additional file 1: Table S1. of Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

description: Expression patterns of MYB genes in different stages of cotton fiber development measured by RNA-seq. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3642821_d21.v1
title: Additional file 1: Table S1. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: Details of the MAGIC maize founder lines. For each line, developer, breeding group, and pedigree are given. Web links to further information and seed availability are provided. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3642821_d20.v1
title: Additional file 13: Table S6. of Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

description: Phenotypic estimated values of the eight founders and 529 MM lines analyzed for days to pollen shed (PS), plant height (PH), ear height (EH), and transformed grain yield (GYrad). (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3642827_d3.v1
title: MOESM4 of DNA methylation signature of human fetal alcohol spectrum disorder

description: Additional file 4: Table S3. Table of differentially methylated regions.
DOI: 10.6084/m9.figshare.c.3642827_d2.v1
title: MOESM3 of DNA methylation signature of human fetal alcohol spectrum disorder

description: Additional file 3: Table S2. Table of genes with multiple differentially methylated probes.
DOI: 10.6084/m9.figshare.c.3642827_d4.v1
title: MOESM6 of DNA methylation signature of human fetal alcohol spectrum disorder

description: Additional file 6: Table S5. Table of imprinted genes in humans.
DOI: 10.6084/m9.figshare.c.3642827_d5.v1
title: MOESM5 of DNA methylation signature of human fetal alcohol spectrum disorder

description: Additional file 5: Table S4. Table of pyrosequencing primers.
DOI: 10.6084/m9.figshare.c.3642827_d6.v1
title: MOESM2 of DNA methylation signature of human fetal alcohol spectrum disorder

description: Additional file 2: Table S1. Table of differentially methylated probes.
DOI: 10.6084/m9.figshare.c.3643124_d2.v1
title: Additional file 1: Table S4. of Investigating associations between biting time in the malaria vector Anopheles arabiensis Patton and single nucleotide polymorphisms in circadian clock genes: support for sub-structure among An. arabiensis in the Kilombero valley of Tanzania

description: The SNP information including flanking sequences and primer sequences used for iPLEX SNP genotyping. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3643154_d1.v1
title: Additional file 10: Table S6. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: EdgeR results from MMGs. Differential expression results calculated by edgeR for MMG counts produced by the stage 2 analysis. Can be downloaded from [43]. (XLSX 428 kb)
DOI: 10.6084/m9.figshare.c.3643154_d3.v1
title: Additional file 8: Table S4. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Counts of multi-map groups (MMGs) from Choi et al. [35]. Counts of reads from Choi et al. that map uniquely to MMGs. Can be downloaded from [43]. (XLSX 876 kb)
DOI: 10.15468/dl.n792mb
title: Occurrence Download

description: A dataset containing 13623 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bagre marinus (Mitchill, 1815)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 13623 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038256-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3643154_d2.v1
title: Additional file 11: Table S7. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: Novel differentially expressed MMGs. The 672 differentially expressed MMGs that do not contain any genes identified as differentially expressed by the stage 1 analysis. Can be downloaded from [43]. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3643154_d4.v1
title: Additional file 9: Table S5. of Errors in RNA-Seq quantification affect genes of relevance to human disease

description: EdgeR results from unique counts. Differential expression results calculated by edgeR for gene counts produced by the stage 1 analysis. Can be downloaded from [43]. (XLSX 2159 kb)
DOI: 10.6084/m9.figshare.c.3643340_d1.v1
title: Additional file 1 of Transcriptome profiling of bovine inner cell mass and trophectoderm derived from in vivo generated blastocysts

description: Table S1. Embryo recovery data. Detail information of in vivo embryo production and ICM/TE immunosurgery. Table S2. Differentially regulated gens. List of genes differentially expressed between ICM and TE of in vivo-derived blastocysts (FDR 2, P ≤ 0.01, FC ≥2). Table S3. ICM/TE predominant gene list. Breakdown of genes exclusively expressed in ICM and TE after filtering data against background genes. Table S4. Epigenetic landscape of ICM transcriptome. Transcriptional profile of epigenetic genes expressed in ICM compared to TE in bovine. Table S5. Effect of in vitro culture on transcriptional profile of ICM and TE. Comparison between transcriptome data of bovine ICM and TE obtained from in vivo (This study) and in vitro (Ozawa et al. [19], and Nagomoto et al. [20]) studies. Table S6. Comparative transcriptional profile of pluripotency related genes between human, mouse and bovine. Expression profile of genes with similar identity between a human [16] study and a mouse study [14] were compared with this study. Table S7. RT-qPCR primers. Sequences (5’–3’) of reverse transcription qRT-PCR-specific primers of candidate genes expressed in bovine embryos. (XLSX 1729 kb)
DOI: 10.6084/m9.figshare.c.3643523_d1.v1
title: MOESM1 of Malaria vector populations across ecological zones in Guinea Conakry and Mali, West Africa

description: Additional file 1. Molecular attribute data for mosquitoes collected across ecological zones in Guinea and Mali.
DOI: 10.6084/m9.figshare.c.3643526_d3.v1
title: MOESM1 of Functional demonstrations of starch binding domains present in Ostreococcus tauri starch synthases isoforms

description: Additional file 1: Table S1. Sequences Retrieved from Similarity Searches.
DOI: 10.6084/m9.figshare.c.3643532_d1.v1
title: Additional file 1: Table S1. of Deciphering mechanisms of drug sensitivity and resistance to Selective Inhibitor of Nuclear Export (SINE) compounds

description: MetaCore analysis of fold changes in expression of all genes in SINE compound-resistant versus parental cells post-treatment. FDR = Benjamini-Hochberg False Discovery Rate. Red = positive, blue = negative, color intensity corresponds to fold change magnitude. Table S2. MetaCore analysis of fold changes in expression of genes with p53 regulatory elements in SINE compound-resistant versus parental cells post-treatment. FDR = Benjamini-Hochberg False Discovery Rate. In the p53 regulation column, “+”, “-“and “?” correspond to positive, negative, and uncertain regulation by p53, respectively. Red = positive, blue = negative, color intensity corresponds to fold change magnitude. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.c.3643535_d1.v1
title: Additional file 1: Table S1. of Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines

description: The mean of AUCs between equations and disease classes in Jamu data. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d2.v1
title: Additional file 9: Table S6. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Primer and sequence information for allele-specific SNP assays. (CSV 597 bytes)
DOI: 10.6084/m9.figshare.c.3643550_d3.v1
title: Additional file 2: Table S1. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Detailed information for each sample used. Sample ID, Barcodes, Read recovered etc. (CSV 12Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d6.v1
title: Additional file 11: Table S7. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Synteny comparisons. Location of each marker retrieved in tested genomes. For each marker, the chromosome ID, start and end location of the best BLASTn hit is reported. (CSV 138Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d4.v1
title: Additional file 6: Table S4. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Female only genetic map (positions and RAD locus sequences). (CSV 122Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d9.v1
title: Additional file 4: Table S3. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Consensus genetic map (positions and RAD locus sequences). (CSV 235Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d8.v1
title: Additional file 3: Table S2. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Full genotypes for mapping family. (CSV 301Â kb)
DOI: 10.6084/m9.figshare.c.3643550_d11.v1
title: Additional file 8: Table S5. of Mapping the sex determination locus in the hÄ puku (Polyprion oxygeneios) using ddRAD sequencing

description: Male only genetic map (positions and RAD locus sequences). (CSV 130Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d4.v1
title: Additional file 18: Table S10. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NZ combination. (XLSX 45Â kb) (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d5.v1
title: Additional file 16: Table S8. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: GO enrichment analysis of global jiDE genes of the NZ combination. (XLSX 53Â kb) (XLSX 49Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d6.v1
title: Additional file 14: Table S6. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: GO enrichment analysis of changed-tissues and global jiDE genes of the NM combination. (XLSX 16Â kb) (XLSX 12Â kb)
DOI: 10.15468/dl.adv7ma
title: Occurrence Download

description: A dataset containing 19081 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bairdiella chrysoura (Lacepède, 1802)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 19081 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038257-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3643793_d9.v1
title: Additional file 13: Table S5. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Expression of transposable element (TE) related genes. (XLSX 45Â kb) (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d12.v1
title: Additional file 22: Table S12. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Commonly detected changed-tissues jiDE genes between the NM and NZ combinations. (XLSX 53Â kb) (XLSX 49Â kb)
DOI: 10.6084/m9.figshare.c.3643793_d15.v1
title: Additional file 23: Table S13. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Details of expression quantitative trait loci (eQTLs) detected global Minghui63-Zhenshan97 differentially expressed (MZDE) genes. (XLSX 45Â kb) (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3643997_d1.v1
title: MOESM5 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 5. Functional characterization of the GBs according to SEED. (“SEED” worksheet) GBs were annotated using SEED subsystem and for each category (row 1) the subcategories are reported (row 2). Numbers refer to the subsystem feature counts. The SEED categories are reported in columns highlighted in grey (C, R, X, AF, AH, AL, AP, AX, BN, BR, BV, BZ, CF, CJ, CO, CV, DG, DN, DT, DW, DZ, EH, ER, EW, FH, FL, FN). In columns at right of each category are reported the results for the subcategories (for example, columns D-Q refer to the “super-category” “C”). Rows 110–114 report the median, the third and the first quartile results for each column. In red and in blue are highlighted the GBs having high and low numbers of subsystem feature counts (those in the third and first quartile of each category). (“hypergeometric” worksheet) For each GB and each SEED functional category the P value obtained from hypergeometric distribution is reported.
DOI: 10.6084/m9.figshare.c.3643997_d2.v1
title: MOESM9 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 9. Metadata regarding the operational conditions of the reactors. Metadata regarding the operational parameters of the reactors including pH, methane yield and volatile fatty acid concentration.
DOI: 10.6084/m9.figshare.c.3643997_d4.v1
title: MOESM2 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 2. Gene annotation. Annotation of the genes identified in the assembly using COG, KEGG and Pfam databases.
DOI: 10.6084/m9.figshare.c.3643997_d5.v1
title: MOESM6 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 6. Functional characterization of the GBs according to COG. (“COG_gene_numb” worksheet) GBs were annotated using COG. Numbers refer to the genes identified on each GB for each COG category. The COG categories are reported in columns (C–AA), the GBs are reported in rows (2–107). (“COG_perc” worksheet) Percentages of genes belonging to COG categories are calculated with respect to the total number of COG results for each GB (note that some genes belong to more than one COG category). In red and green are highlighted, for each COG category, the GBs having the 10 highest and the 10 lowest percentages. (“hypergeometric” worksheet). For each GB and each COG functional category, the P value obtained from hypergeometric distribution is reported.
DOI: 10.6084/m9.figshare.c.3643997_d6.v1
title: MOESM7 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 7. Functional characterization of the GBs according to KEGG. (“KEGG” worksheet) GBs were annotated using KEGG. Numbers refer to the genes identified on each GB for each KEGG pathway. The KEGG pathways are reported in columns (C–EZ), the GBs are reported in rows (2–107). (“hypergeometric” worksheet) For each GB and each KEGG pathway, the P value obtained from hypergeometric distribution is reported.
DOI: 10.6084/m9.figshare.c.3643997_d7.v1
title: MOESM8 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 8. Database resources used for functional characterization of the GBs. Functional processes of the GBs analyzed in the AD community are reported in the first column. The SEED subsystems, KEGG pathway maps, COG categories and Pfam domains used are reported in columns 3 and 4.
DOI: 10.6084/m9.figshare.c.3643997_d10.v1
title: MOESM3 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 3. Taxonomy assignment and characteristics of the GBs. The taxonomy of the GBs identified was determined using different methods and a taxonomic assignment was suggested considering the results obtained. In columns (A–V) are reported: (A) the acronym of the GBs as reported in the main text (Sp = Spirochetes; Sy = Synergistetes; Th = Thermotogae; Pr = Proteobacteria; Fi = Firmicutes; Te = Tenericutes; Ac = Actinobacteria; Ba = Bacteroidetes; Tm = TM7 phylum; Eu = Euryarchaeota) the Phylum was determined using Phylophlan and, secondly, the results obtained from BLASTP search versus nr databases filtered using MEGAN; (B) the tentative taxonomic assignment; (C) domain of the genome bin; (D) phylum; (E) taxonomic level considered for the name assignment (the result obtained using Phylopythia was used when more than 50 % of the genome bin sequence was assigned to the same taxonomic group); (F) confidence for taxonomic assignment obtained using Phylophlan; (G–I) domain, phylum, class determined using Phylophlan; (J) taxonomic assignment determined using Phylopythia; (K) percentage of the genome assigned as reported in “J”; (L) taxonomic level reported in “J”; (M) number of genes having BLASTP e-value lower than 1*E-5; (N) average similarity for BLASTP results; (O) number of genes having BLASTN e-value lower than 1*E-5; (P) average similarity for BLASTN results; (Q) the species having the highest number of best match in BLASTP column “M”; (R) taxonomy assignment obtained using RDP classifier on the 16S rRNA gene, similarity, contig where the 16S gene was identified; (S) total length of the scaffolds assigned to the genome bin; (T) number of scaffolds, (U) scaffolds N50, (V) scaffolds N90, (W) average scaffolds length, (X) number of contigs determined after splitting scaffolds on stretched of 10 or more unknown bases “N”, (Y) contigs N50, (Z) contigs N90, (AA) average contigs length, (AB) number of protein encoding genes identified using SEED subsystem; (AC) number of protein encoding genes identified using Prodigal; (AD) total number of essential genes identified, (AE) univocal number of essential genes (removed those in multiple copies); (AF) estimated completeness of the GB; (AG) average number of essential genes in phylum 1. Bold text in columns (A, U, Y, Z, AA, AF) refers to GBs that satisfy the Human Microbiome Project quality criteria; (AH) estimated contamination level determined considering the univocal number of essential genes and the total number of essential genes in multiple copies; (AI) estimated completeness of the GB determined using CheckM software; (AJ) estimated level of contamination determined using CheckM software.
DOI: 10.6084/m9.figshare.c.3643997_d8.v1
title: MOESM10 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 10. Suggested viewer: FigTree http://tree.bio.ed.ac.uk/software/figtree/ . Newick format of the file representing the microbial tree of life. The tree reports the 106 GBs of the AD microbial community together with other 3,737 microbial genomes. The file was obtained with PhyloPhlAn using 400 broadly conserved proteins used to extract phylogenetic signal.
DOI: 10.6084/m9.figshare.c.3643997_d9.v1
title: MOESM4 of Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

description: Additional file 4. Input files used for the network Representation of the Biogas Functional Organization (NRBFO). Functional analysis of the microbial community begins with the identification of the GBs enriched in SEED subsystem counts (ranked among the top one eighth of each SEED category). Starting from the entire list of SEED sub-categories (Data Set 6) 56 were selected (the more relevant for the characterization of the biogas community) and the GBs with high number of subsystem counts were identified (“node abundance” worksheet). The subsystem categories were compared in order to identify if they shared the same GBs and the couples with three or more common genome bins were identified (“edge_size_connections” worksheet). The number of GBs identified for each category was used to set the node size and the number of GBs shared was used to set the edge size (Fig. 2).
DOI: 10.6084/m9.figshare.c.3644210_d7.v1
title: Additional file 6: Table S2. of Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

description: Domains in all expressed transcripts. Batch CD-Search was used for large-scale conserved domain search of all expressed transcripts during soybean embryo development. (XLSX 22764 kb)
DOI: 10.6084/m9.figshare.c.3644210_d9.v1
title: Additional file 7: of Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

description: The â  noncoding.faâ   file. This FASTA file contains all lncRNA transcripts and their sequences identified in developing soybean embryos. (FA 32275 kb)
DOI: 10.6084/m9.figshare.c.3644210_d10.v1
title: Additional file 10: Table S4. of Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

description: Pearson correlations between sense and antisense transcript pairs. (A) All identified sense and antisense transcript pairs. (B) Correlations between known sense (class “=”) and antisense (classes “x” and “s”) transcripts. (XLSX 199 kb)
DOI: 10.5281/zenodo.13070596
title: A Network-Based Phase-Gradient Stacking Method for Resolving Long-wavelength deformation from low-coherence SAR interferograms

description: This dataset includes the key results, primary InSAR and GNS observatons  in our study.
DOI: 10.5281/zenodo.13070597
title: A Network-Based Phase-Gradient Stacking Method for Resolving Long-wavelength deformation from low-coherence SAR interferograms

description: This dataset includes the key results, primary InSAR and GNS observatons  in our study.