cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3596984_d3
title: Additional file 2: Figures S1a-c. of Lack of direct evidence for natural selection at the candidate thrifty gene locus, PPARGC1A

description: Tajima’s D calculated across chromosome 4 using a 30 kbp sliding window by population. Chromosome 4:22.7–24.9 Mbp is shown with chromosome mean (blue) and 2.5%, 97.5% quantiles (purple) from Table 4 marked. Location of PPARGC1A is marked in red. Rs8192678 is marked by a red dashed line. Figure S1b Tajima’s D calculated across chromosome 4 using a 5 kbp sliding window by population. Chromosome 4:22.7–24.9 Mbp is shown with chromosome mean (purple) and 2.5%, 97.5% quantiles (purple) from Table 4 marked. Location of PPARGC1A is marked in red. Rs8192678 is marked by a red dashed line. Figure S1c Tajima’s D calculated across chromosome 4 using a 1 kbp sliding window by population. Chromosome 4:22.7–24.9 Mbp is shown with chromosome mean (blue) and 2.5%, 97.5% quantiles (purple) from Table 4 marked. Location of PPARGC1A is marked in red. Rs8192678 is marked by a red dashed line. (ZIP 1473 kb)
DOI: 10.6084/m9.figshare.c.3596966_d5
title: Additional file 2: of Spatiotemporal variation of mammalian protein complex stoichiometries

description: Table listing the protein complex resource. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.c.3596987_d3
title: Additional file 6: of Blood lipids influence DNA methylation in circulating cells

description: Polygenic scores constructed from lipid GWAS-identified SNPs associate strongly with their respective lipid levels but explain only a small amount of their variance. (CSV 104 bytes)
DOI: 10.6084/m9.figshare.c.3597077_d1
title: Additional file 2: of High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing

description: Sequence information of the mapped SNP markers. (XLSX 657Â kb)
DOI: 10.6084/m9.figshare.c.3597077_d2
title: Additional file 1: of High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing

description: Total SLAFs. (XLSX 16699Â kb)
DOI: 10.6084/m9.figshare.c.3597077_d3
title: Additional file 3: of High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing

description: Detailed SNP marker information for each of the twelve linkage groups. (XLSX 113Â kb)
DOI: 10.6084/m9.figshare.c.3597086_d1
title: MOESM2 of Significant association and synergistic adverse prognostic effect of podocalyxin-like protein and epidermal growth factor receptor expression in colorectal cancer

description: Additional file 2. Comparison of EGFR protein expression in CRC assessed by two different antibodies in cohort 1.
DOI: 10.6084/m9.figshare.c.3597086_d2
title: MOESM1 of Significant association and synergistic adverse prognostic effect of podocalyxin-like protein and epidermal growth factor receptor expression in colorectal cancer

description: Additional file 1. Patient and tumour characteristics in the three cohorts.
DOI: 10.6084/m9.figshare.c.3597203_d1
title: Additional file 2: Table S3. of Evolution of the Tim17 protein family

description: The phylogenetic tree of Tim17 family proteins in Newick format. (TXT 301 kb)
DOI: 10.6084/m9.figshare.c.3597209_d1
title: Additional file 4: Table S4. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: GO annotation counts for the assembled transcripts. Summary of retrieved GO annotations for de novo assembled, restructured transcripts. (XLS 263 kb)
DOI: 10.6084/m9.figshare.c.3597203_d3
title: Additional file 1: Table S1. of Evolution of the Tim17 protein family

description: The list of sequences obtained by the Tim17 protein family-specific HHsearch in Uniprot database of reference proteomes. The columns A to E - taxonomic affiliation, the column F- sequence ID, the column F – sequence description, the column H - the affiliation to particular groups of Tim17 protein family (Nogroup indicates that the sequence could not be assigned to any defined subgroups), the column I- the amino acid sequence. (XLS 2637 kb)
DOI: 10.6084/m9.figshare.c.3597209_d2
title: Additional file 2: Table S2. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: BLASTx hits of transcripts. BLASTx top hit results for de novo assembled contigs of restructured transcripts. (XLS 4120 kb)
DOI: 10.6084/m9.figshare.c.3597209_d3
title: Additional file 9: Table S8. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: Enriched GO terms for DE transcripts clustered by expression patterns. Listing of GO terms enriched for k-means clustered expression patterns of DE transcripts with description, number transcripts, and p-value. (XLS 27 kb)
DOI: 10.6084/m9.figshare.c.3597203_d4
title: Additional file 4: Table S2. of Evolution of the Tim17 protein family

description: The overall distribution of Tim17 family protein in eukaryotes. (XLS 135 kb)
DOI: 10.6084/m9.figshare.c.3597221_d1
title: Additional file 6: of Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

description: Calculation on the population genetic distance among the three species carrying A genome by resampling. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.c.3597224_d1
title: Additional file 1: Table S1. of Phylogenetic and comparative genomics of the family Leptotrichiaceae and introduction of a novel fingerprinting MLVA for Streptobacillus moniliformis

description: Analysis of clusters of orthologous groups (COGs) of the Leptotrichiaceae members used in this study. COGs were assessed as described in the Materials and Methods. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3597209_d4
title: Additional file 12: Table S11. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: Putative sRNA/target pairs identified from negatively correlated DE sRNAs and DE transcripts. Listing of sRNA/target pairs based on negative correlation of DE sRNA and DE transcript expression patterns that were identified using psRNATarget [58]. Stage transitions of DE, correlation coefficient, and transcript BLASTx top hits are listed. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3597221_d2
title: Additional file 1: of Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

description: Information of DArT-seq markers and genotypes of the SY-PM genetic mapping population of B. juncea. (XLSX 6076Â kb)
DOI: 10.6084/m9.figshare.c.3597209_d5
title: Additional file 10: Table S9. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: DE sRNAs in T1 and T2. Listing of identifiers of DE sRNA up- and downregulated in the stage transitions. (XLS 349 kb)
DOI: 10.6084/m9.figshare.c.3597209_d6
title: Additional file 11: Table S10. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: Sequences of DE sRNAs and predicted miRNAs. Listing of all DE sRNAs as well as miRNAs with their sRNA identifier (XLS 1022 kb)
DOI: 10.6084/m9.figshare.c.3597221_d3
title: Additional file 3: of Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

description: The copies of ancestral blocks of Brassicaceae discriminated in Brassica species and Brassica subgenomes. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3597209_d7
title: Additional file 8: Table S7. of Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”

description: Enriched GO terms for DE transcripts in the stage transitions. Listing of GO terms enriched for DE transcripts in stage transitions seperately for up- and downregulated expression patterns with term description, number of transcripts, and p-value. (XLS 35 kb)
DOI: 10.6084/m9.figshare.c.3597308_d1
title: MOESM2 of Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

description: Additional file 2. OrthoMCL and functional annotation, methylome, DarkHorse, subcellular targeting. ND (no data) indicates data not sufficient enough to determine a value.
DOI: 10.6084/m9.figshare.c.3597314_d1
title: Additional file 2: of Modelling the effect of short-course multidrug-resistant tuberculosis treatment in Karakalpakstan, Uzbekistan

description: Model code for Matlab 2015b. (ZIP 10 kb)
DOI: 10.6084/m9.figshare.c.3597290_d4
title: Additional file 4: of Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations

description: GO biological processes highly significantly enriched in the 513 preselected gene set for ADC. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3597308_d3
title: MOESM4 of Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

description: Additional file 4. Triose phosphate transporters, accession numbers for sequences used in Fig.Â 9 and Additional file 1: Figure S2.
DOI: 10.6084/m9.figshare.c.3597290_d5
title: Additional file 3: of Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations

description: Preselected 150 candidate genes for SCC. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3597308_d4
title: MOESM3 of Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

description: Additional file 3. Periplastid predictedÂ genes.
DOI: 10.6084/m9.figshare.c.3597290_d6
title: Additional file 2: of Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations

description: Preselected 513 candidate genes for ADC. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.c.3597323_d4
title: Additional file 7: Table S4. of Combining RNA-seq and proteomic profiling to identify seminal fluid proteins in the migratory grasshopper Melanoplus sanguinipes (F)

description: Predict secreted proteins based on the presence of a signal peptide (SP) or by non-classical secretory pathways (NC) (Scoring functionâ  &gt;â  0.5). Expression patterns using qualitative RT-PCR to proteins with SP [(a) Male expression exclusively; (b) Expression in both sexes and (c) Not amplified. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.c.3597323_d5
title: Additional file 3: Table S2. of Combining RNA-seq and proteomic profiling to identify seminal fluid proteins in the migratory grasshopper Melanoplus sanguinipes (F)

description: Primers used in RT-PCR and PCR conditions. PCR was performed with the following thermal conditions 60 s at 95 °C, 50 s at 94 °C, 30 s at 62 °C, 3 cycles /°C declining over a range at 1 °C intervals of 30 s, 72 s at 60 °C, 50 s at 95 °C, 30 s at 60 °C, 6 cycles /°C declining over a range at 0.5 °C intervals of 30 s, 50 s at 95 °C, 30 s at 56 °C, 30 cycles of 30 s and 60 s at 72 °C. Relative expression was not quantified. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3597323_d6
title: Additional file 2: Table S1. of Combining RNA-seq and proteomic profiling to identify seminal fluid proteins in the migratory grasshopper Melanoplus sanguinipes (F)

description: Melanoplus sanguinipes Seminal fluid proteins identified by mass-spectrometry. Predicted function based on the annotation and BLAST2GO. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.c.3597428_d2
title: Additional file 1: Table S1. of Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells

description: Primer sequences for qPCR analysis w/o RA and JQ1 treatment (from Fig.Â 4B) (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3597446_d1
title: MOESM1 of Malaria in pregnancy: a passive surveillance study of pregnant women in low transmission areas of Colombia, Latin America

description: Additional file 1. Parasite genotypes from pregnant women samples.
DOI: 10.6084/m9.figshare.c.3597449_d1
title: Additional file 2: of An external validation of models to predict the onset of chronic kidney disease using population-based electronic health records from Salford, UK

description: R script to test QKidneyÂŽ. (R 7.88 kb)
DOI: 10.6084/m9.figshare.c.3597428_d3
title: Additional file 7: Table S2. of Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells

description: The overlapping peaks of Brd4 with TFs in ESCs within 1Kbps. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3597449_d3
title: Additional file 1: of An external validation of models to predict the onset of chronic kidney disease using population-based electronic health records from Salford, UK

description: Read codes used to extract the data from the Salford Integrated Record. (CSV 518 kb)
DOI: 10.6084/m9.figshare.c.3597515_d15
title: Additional file 18: of The transcriptome of metamorphosing flatfish

description: In-house database of candidate genes involved in thyroid gland development/thyroid hormone (TH) metabolism and signaling, including transcripts with a relevant role in TH synthesis, transport and activity. Protein name, Symbol, Accession number (no.), Organism and Biological role are shown. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3597548_d2
title: Additional file 4: Table S2. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

description: Genomic position and corresponding gene IDs of the SSR and SNP markers in the Wm82.a2.v1 assembly, the SSR and SNP markers were from the BARCSOYSSR_1.0 database (Song et al. [30]). (XLS 8876 kb)
DOI: 10.6084/m9.figshare.c.3597548_d3
title: Additional file 1: Table S1. of Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

description: NCBI ssID, SNP ID of SoySNP50K SNPs (Song et al. [23]), genome position Glyma1.01, corresponding genome position in the Wm82.a2.v1 assembly, gene IDs of SNPs in the Wm82.a2.v1 assembly and genetic linkage group and linkage position of the SNPs in the Williams 82 x PI479752 (WP) and Essex x Williams 82 (EW) populations (XLS 10149 kb)
DOI: 10.6084/m9.figshare.c.3597566_d1
title: Additional file 2: Figures S1, S2. of Analyzing video recorded support of postnatal transition in preterm infants following a c-section

description: The time point of first occurrence of an intervention for every LGA, VLGA and ELGA that the specific intervention was given. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.c.3597563_d2
title: MOESM4 of In silico search, characterization and validation of new EST-SSR markers in the genus Prunus

description: Additional file 4: Table S1. Description of SSR containing ESTs with significant matches in Prunus species, including accession numbers, repeat motif, primer sequences, product size, and annealing temperature. In addition, position and associated genes with respect to the reference genomes of mei and peach has been added. EST-SSR marked by asterisk has been previously described by Chen et al. [13].
DOI: 10.6084/m9.figshare.c.3597566_d2
title: Additional file 4: Figure S3. of Analyzing video recorded support of postnatal transition in preterm infants following a c-section

description: Duration of every intubation attempt (successful and unsuccessful) according to the GA. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.c.3597515_d19
title: Additional file 19: of The transcriptome of metamorphosing flatfish

description: In-house database of candidate genes involved in TH signaling/metabolism identified in Xenopus laevis in previously published literature [84, 86, 87, 134]. Protein name, Symbol, Accession number (no.), Organism and References are shown. (XLSX 29 kb)
DOI: 10.15468/dl.yh29mw
title: Occurrence Download

description: A dataset containing 214 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Salvadora mexicana (Duméril, Bibron & Duméril, 1854)"
 ]
}

 The dataset includes 214 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032644-241126133413365/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.3597656_d4
title: Additional file 20: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

description: Title: Sub-genome specific primer names and their sequences used in this study for RT-qPCR gene expression. Description of data: This file contains 19 RT-qPCR primer pair sequences that were used to analyze gene expression near the major QTL on chromosome A07. Corresponding gene name and descriptions are also included here. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3597707_d1
title: Additional file 1: of A genome-wide analysis in cluster headache points to neprilysin and PACAP receptor gene variants

description: Supplemental Methods. Table S1. list of selected candidate genes, GO terms annotations, number of rare protein altering variants (PAV) contained in each gene, and gene-level P-values obtained from SKAT analysis. Table S2. list of rare PAV (MAFâ
DOI: 10.6084/m9.figshare.c.3597656_d8
title: Additional file 15: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

description: Title: Annotated genes within 71 M bp and 76 M bp region of chromosome A07 and their RNA-seq data. Description of data: This table contains gene name and associated annotation near the detected loci on chromosome A07. The RNA-seq data from our previous studies for the gene are also included in this table. First column have the gene name followed by physical location, Arabidopsis ortholog gene, gene description and RPKM value of RNA-seq data for the different RNA libraries. (XLSX 75 kb)
DOI: 10.6084/m9.figshare.c.3597809_d1
title: Additional file 7: of Maternal care in Acanthosomatinae (Insecta: Heteroptera: Acanthosomatidae)—correlated evolution with morphological change

description: Format: nexus. Title: Data matrix for likelihood reconstruction of ancestral state of the two traits (maternal care and Pendegrast’s organ) on 34 species with confirmed behavior data. (NEX 16 kb)
DOI: 10.6084/m9.figshare.c.3597809_d2
title: Additional file 4: of Maternal care in Acanthosomatinae (Insecta: Heteroptera: Acanthosomatidae)â  correlated evolution with morphological change

description: Format: nexus. Title: Data matrix of aligned sequences for Bayesian analysis. (NEX 130Â kb)
DOI: 10.6084/m9.figshare.c.3597809_d3
title: Additional file 3: of Maternal care in Acanthosomatinae (Insecta: Heteroptera: Acanthosomatidae)—correlated evolution with morphological change

description: Format: XLS. Title: Species sequenced in the study, behavioral data, and condition of Pendergrast’s organ on the pregenital segments. Legend: Symbols: + (present), − (absent), R (reduced). 1This species is conspecific with Acanthosoma giganteum Matsumura, recently synonymized by Tsai & Rédei [53]; the junior synonymous name, A. giganteum, is frequently cited, and its mitochondrial gene of cytochrome oxidae subunit I (mtDNA-COI) is also available from GenBank (AB368853). 2An undescribed species closely related to S. javanensis Distant. Collection abbreviation: JFT– Jing-Fu Tsai’s coll. deposited in systematic laboratory of Hokkaido University, Sapporo, Japan; NKU– Department of Zoology and Developmental Biology, Nankai University, Tianjin, China. LC099108–LC099371: Genbank accession numbers. (XLS 56 kb)
DOI: 10.6084/m9.figshare.c.3597803_d2
title: Additional file 1: Table S1. of Immune genes and divergent antimicrobial peptides in flies of the subgenus Drosophila

description: PCR primers used in expression analyses and amplification of immune gene DNA from diverse Drosophila. (XLSX 39Â kb)
DOI: 10.6084/m9.figshare.c.3597812_d2
title: Additional file 2: of Tetrapod V1R-like ora genes in an early-diverging ray-finned fish species: the canonical six ora gene repertoire of teleost fish resulted from gene loss in a larger ancestral repertoire

description: A table containing gene names, protein sizes, genomic locations, Genbank IDs, NCBI reference sequences, first publications and previously reported names of ora/v1r genes of ray-finned fish, elephant shark and African coelacanth. (XLS 44 kb)
DOI: 10.6084/m9.figshare.c.3597809_d4
title: Additional file 5: of Maternal care in Acanthosomatinae (Insecta: Heteroptera: Acanthosomatidae)—correlated evolution with morphological change

description: Format: XLS. Title: Data matrix for character evolution. Legend: Data matrix for character evolution. Character 1, egg-nymph guarding behaviour (maternal care) [0 = absent, 1 = present, ? = missing data]. Character 2, Pendergrast’s organ [0 = absent, 1 = present, 2 = reduced]. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3597803_d3
title: Additional file 5: Table S2. of Immune genes and divergent antimicrobial peptides in flies of the subgenus Drosophila

description: Net charges of DptA or DptC domains from Drosophila diptericins. Net charges were calculated using Protein Calculator v3.4 (http://protcalc.sourceforge.net/), and are given for each domain. DptC shows extensive differences at the amino acid sequence level. These differences have resulted in more extreme charges on each domain in the DptC molecule. DptC molecules generally have more negative P domains (except for D. albomicans), and more positive G domains, resulting in relatively similar net charges to DptA (except for D. albomicans). (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.c.3597812_d4
title: Additional file 5: of Tetrapod V1R-like ora genes in an early-diverging ray-finned fish species: the canonical six ora gene repertoire of teleost fish resulted from gene loss in a larger ancestral repertoire

description: Tables containing dN/dS values for all codons of ora1-6 genes of ray-finned fish. (XLS 207 kb)
DOI: 10.6084/m9.figshare.c.3597809_d5
title: Additional file 8: of Maternal care in Acanthosomatinae (Insecta: Heteroptera: Acanthosomatidae)—correlated evolution with morphological change

description: Format: XLS. Title: Data matrix for correlation analysis. Legend: Data matrix for correlation analysis between maternal care and Pendergrast’s organ. Character 1, egg-nymph guarding behaviour (maternal care) [0 = absent, 1 = present]. Character two, Pendergrast’s organ [0 = absent or reduced, see explanation in Methods, 1 = present]. (XLS 31 kb)
DOI: 10.25345/c5bv7b71n
title: MassIVE MSV000096652 - GNPS - Porewater sampling test
title: Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA). LC-MS/MS data acquired in positive mode.
DOI: 10.6084/m9.figshare.c.3597884_d6
title: Additional file 2: of Initiator tRNA genes template the 3′ CCA end at high frequencies in bacteria

description: Structurally aligned data for subset of tRNAs with CAU anticodons, also containing TFAM scores with Silva model in “aligned FastA” format. (FAS 3 MB)
DOI: 10.6084/m9.figshare.c.3597884_d7
title: Additional file 8: of Initiator tRNA genes template the 3â ˛ CCA end at high frequencies in bacteria

description: Perl script for structural reannotation of 3â  ends. (TXT 5 kb)