cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9782513.v1
title: Additional file 1: of Genetic variants in Forkhead box O1 associated with predisposition to sepsis in a Chinese Han population

description: Table S1. The detail information of sepsis special SNPs after initial screening. After whole exome sequencing, synonymous mutations were removed. SNPs only existed in more than 5 sepsis patients and quality score of these SNPs were higher than 95% were selected. The excel file of Table S1 has been submitted as a separate supplementary dataset. (XLS 119 kb)
DOI: 10.6084/m9.figshare.6112565
title: Tandem 3′ UTR Patterns and Gene Expression Profiles of Marc-145 Cells During PRRSV Infection

description: We
conducted research on high-flux transcriptome regarding alternative
polyadenylation and host gene expression regulatory function in the process of PRRSV-infected Marc-145 cells. We used SAPAS method combined with <i>in vitro </i>transcription and obtained 332 million 3’ UTR sequencing reading
segments. These series were enriched with 3’ UTR length polymorphism, gene
expression quantity and other important information.
DOI: 10.6084/m9.figshare.25239952
title: RepeatMasker outfile from Solea senegalensis genome

description: Pleuronectiformes are flatfishes with high commercial value and a prominent example of successful marine adaptation through chromosomal evolution. Hence, the aim of this study was to analyze the relative abundance of repetitive elements in the genome of 10 fish species (8 flatfish) delving into the study of the species of special relevance, Senegalese sole, Solea senegalensis. The results showed differences in the abundance of repetitive elements, with S. senegalensis exhibiting the highest frequency and coverage of these elements reaching the 40% of the genome and not at random distribution. It is noteworthy the presence of relevant peaks of Helitrons in centromeric/pericentromeric positions mainly in the bi-armed chromosomes 1, 2, 4, 6, 7, and 9. The position of the centromeres of this species determined through the genomic localization of the family of satellite DNA PvuII, and other repetitive sequences was obtained de novo. This allowed us to know the genomic position of the centromeres in 19 out of the 21 chromosomes of S. senegalensis. Helitrons showed an accumulation of tandem copies mainly in the pericentromeric positions of chromosomes 1 and 2, occupying a region, in the first case, of 600Kb of tandem repeats. That has only been previously described in mammals and plants. Divergence and copy number studies indicated the possible presence of active families in the species’ genome and the existence of two important events of transposon activity (burst) in the genome of S. senegalensis, mainly accentuated in Helitrons. The results showed that only the families of DNA transposons exhibited a landscape with symmetrical bell-shaped distribution. The phylogenetic analysis of Helitron families revealed the presence of two large groups of families and the presence of four groups of sequences with heterogeneous distribution among chromosomes. Finally, the phylogenomic analysis of 8615 sequences belonging to Helitron insertions from 5 families of flatfish and two external species, allowed to classify the copies into nine groups of sequences with different levels of divergence and clusters, including some branches with distant phylogenetically species. The implications of this study will help to expand the knowledge of chromosome structure and evolution of these species
DOI: 10.6084/m9.figshare.23938464
title: <b>A theropod tooth from the Middle Jurassic of Tibetan Plateau reveals convergent evolution of dromaeosaurid dental morphology</b>

description: <b>The Tibetan Plateau is among the least explored areas in terms of dinosaur paleontology in the world. Here we report a dromaeosaurid-like tooth from the Middle Jurassic Dongdaqiao Formation at the eastern part of the plateau. The tooth shows some dromaeosaurid dental features, including the absence of constriction at the cervix, a relatively small crown base ratio, a strongly recurved apex and lack of large transverse, and marginal undulations. Parsimony phylogenetic analyses using both dentition-based and complete morphological matrices support a dromaeosaurid affinity for this tooth, and place this Tibetan theropod as the sister taxon to </b><i><b>Velociraptor</b></i><b>. However, Bayesian tip dating analyses based on the velociraptorine affinity of the Tibetan tooth place the majority of the diversifications of early-diverging Paravian, particularly of dromaeosaurids, within or earlier than the Middle Jurassic, which is in conflict with the known paravian fossil records. Furthermore, our discriminate analysis based on morphometric data place the Tibetan theropod within Metriacanthosauridae. These results may suggest that the broad resemblances between the Tibetan specimen and velociraptorine teeth is due to convergent evolution. Other dromaeosaurid-like teeth reported from the Middle and Late Jurassic deposits of several sites in Asia and Europe are thus probably nondromaeosaurids as the Tibetan tooth is. Collectively, these suggest the presence of an early diverged theropod lineage with a wide geographical distribution and probably a dromaeosaurid-like dietary niche. This study highlights the importance of using multiple lines of data to identify fragmentary fossils.</b>
DOI: 10.6084/m9.figshare.17120273.v1
title: Additional file 3 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 3: Table S3. The cis-acting elenment in the promoter of PeGT43s.
DOI: 10.6084/m9.figshare.21317139
title: Differentially expressed genes of M. anguillicaudatus_F_muscle-vs-M_muscle

description: Differentially expressed genes between female and male muscles of loach
DOI: 10.6084/m9.figshare.8207315
title: Additional file 2: of Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations

description: Table S2. General properties of 16S rRNA genes of Acidithiobacillus isolates and clones available in the public database. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.8207336
title: Additional file 5: of Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations

description: Table S7. Gene content of genomic regions associated with carboxysome and nitrogenase in Acidithiobacillus strains. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.21317349
title: Differentially expressed genes of C. semilaevis F_brain-vs-M_brain

description: Differentially expressed genes between female and male brains of half-smooth tongue sole
DOI: 10.5281/zenodo.10528309
title: Images of minirhizotron 3 and 4 during 2022 and 2023 in Schifflange (Luxembourg)
DOI: 10.5281/zenodo.10528310
title: Images of minirhizotron 3 and 4 during 2022 and 2023 in Schifflange (Luxembourg)
DOI: 10.6084/m9.figshare.17120294
title: Additional file 8 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 8: Table S6. Cell wall-associated genes (PCC &gt; 0.8) used for co-expression network construction.
DOI: 10.6084/m9.figshare.17120276
title: Additional file 4 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 4: Table S4. The potential transcription factors binding to the promoter of PeGT43s.
DOI: 10.6084/m9.figshare.21317439
title: Differentially expressed genes of C. semilaevis F_muscle-vs-M_muscle

description: Differentially expressed genes between female and male muscles of half-smooth tongue sole
DOI: 10.6084/m9.figshare.8207315.v1
title: Additional file 2: of Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations

description: Table S2. General properties of 16S rRNA genes of Acidithiobacillus isolates and clones available in the public database. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.11353046
title: Additional file 4. Partitioning scheme, evolutionary models and alignments used for phylogenetic and selection analyses. from Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of <i>Gammarus pisinnus</i> and <i>Gammarus lacustris</i>

description: We hypothesized that the mitogenome of <i>Gammarus lacustris</i> (GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of <i>Gammarus pisinnus</i> (GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200–1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55% <i>atp8</i> to 76.1% <i>cox1</i>). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but ‘heterogeneous’ CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, <i>pisinnus</i> and <i>fossarum</i> exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in <i>atp8</i>) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining <i>Gammarus</i> species populating the same geographical range as GP.
DOI: 10.6084/m9.figshare.17120258.v1
title: Additional file 12 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 12: Table S9. The coding sequences and upstream sequences isolated in this study.
DOI: 10.6084/m9.figshare.17120252
title: Additional file 11 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 11: Table S8. Primers used for Y1H expression vector construction.
DOI: 10.6084/m9.figshare.17120267
title: Additional file 2 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 2: Table S2. Ka / Ks and divergence time analysis of PeGT43s pairs.
DOI: 10.6084/m9.figshare.17120276.v1
title: Additional file 4 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 4: Table S4. The potential transcription factors binding to the promoter of PeGT43s.
DOI: 10.6084/m9.figshare.21317451
title: Differentially expressed genes of P. fulvidraco F_muscle-vs-M_muscle

description: Differentially expressed genes between female and male muscles of yellow catfish
DOI: 10.6084/m9.figshare.21317454
title: Differentially expressed genes of P. fulvidraco F_brain-vs-M_brain

description: Differentially expressed genes between female and male brains of yellow catfish
DOI: 10.6084/m9.figshare.12926078
title: Additional file 2 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 2: Table S1. Phenotypic distribution range of three yield-related traits among 315 upland cotton accessions.
DOI: 10.6084/m9.figshare.17120258
title: Additional file 12 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 12: Table S9. The coding sequences and upstream sequences isolated in this study.
DOI: 10.6084/m9.figshare.12923327
title: Additional file 2 of LncRNA PSMB8-AS1 contributes to pancreatic cancer progression via modulating miR-382-3p/STAT1/PD-L1 axis

description: Additional file 2: Table 2. The characteristics of the primers used in real-time PCR and plasmid sequence.
DOI: 10.6084/m9.figshare.17120252.v1
title: Additional file 11 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 11: Table S8. Primers used for Y1H expression vector construction.
DOI: 10.6084/m9.figshare.12923327.v1
title: Additional file 2 of LncRNA PSMB8-AS1 contributes to pancreatic cancer progression via modulating miR-382-3p/STAT1/PD-L1 axis

description: Additional file 2: Table 2. The characteristics of the primers used in real-time PCR and plasmid sequence.
DOI: 10.6084/m9.figshare.12926069.v1
title: Additional file 11 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 11: Table S10. Information of the 315 upland cotton accessions.
DOI: 10.6084/m9.figshare.12926072
title: Additional file 12 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 12: Table S11. The elastic GSC matrix and GSC eigenvectors.
DOI: 10.6084/m9.figshare.12926078.v1
title: Additional file 2 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 2: Table S1. Phenotypic distribution range of three yield-related traits among 315 upland cotton accessions.
DOI: 10.6084/m9.figshare.12926090
title: Additional file 6 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 6: Table S5. A total of 115 genes annotated in the six adjacent genome fragments of the stable SNPLDB loci.
DOI: 10.6084/m9.figshare.17120261.v1
title: Additional file 1 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 1: Table S1. Basic characteristics of proteins encoded by GT43 genes in five bamboo species.
DOI: 10.6084/m9.figshare.8207495.v1
title: MOESM1 of LncRNA H19 regulates PI3Kâ Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network

description: Additional file 1. The differentially expressed mRNAs, lncRNAs, pseudogenes, and miRNA in CRC.
DOI: 10.6084/m9.figshare.12926069
title: Additional file 11 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 11: Table S10. Information of the 315 upland cotton accessions.
DOI: 10.6084/m9.figshare.12926081
title: Additional file 3 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 3: Table S2. The correlation analysis among three yield-related traits.
DOI: 10.6084/m9.figshare.12926096
title: Additional file 8 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 8: Table S7. The GO results of 16 potential candidate genes controlling target traits.
DOI: 10.6084/m9.figshare.12926096.v1
title: Additional file 8 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 8: Table S7. The GO results of 16 potential candidate genes controlling target traits.
DOI: 10.6084/m9.figshare.12926081.v1
title: Additional file 3 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 3: Table S2. The correlation analysis among three yield-related traits.
DOI: 10.6084/m9.figshare.12926099.v1
title: Additional file 9 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 9: Table S8. The KEGG results of 16 potential candidate genes controlling target traits.
DOI: 10.6084/m9.figshare.21317469
title: Differentially expressed genes of O. niloticus F_muscle-vs-M_muscle

description: Differentially expressed genes between female and male muscles of Nile tilapia
DOI: 10.6084/m9.figshare.15020636
title: Additional file 1 of Investigating causal relationships between exposome and human longevity: a Mendelian randomization analysis

description: Additional file 1: Table S1. Details of the instruments used as proxy risk factors for longevity. Table S2. Description of independent exposure GWAS used in validation. Table S3. Estimates of inverse variance weighted method for significant associations between genetically predicted exposures and longevity. Table S4. Sensitivity analysis results for the metabolites identified in secondary analysis. Table S5. Pleiotropy and heterogeneity analyses for the association between exposures and Alzheimer's disease in secondary analysis. Table S6. The Mendelian randomization association of individual SNPs of screening traits in primary analysis. Table S7. Mendelian randomization results of validation using independent exposure GWAS. Table S8. Mendelian randomization results of validation using dataset of 90th percentile longevity. Table S9. Mendelian randomization results of validation using dataset of 99th percentile longevity. Table S10. List of exposures in the present study. Table S11. Exposures identified significantly and suggestively associated with 90th percentile longevity in primary analyses. Table S12. Exposures identified significantly and suggestively associated with 99th percentile longevity in secondary analyses.
DOI: 10.6084/m9.figshare.17120273
title: Additional file 3 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 3: Table S3. The cis-acting elenment in the promoter of PeGT43s.
DOI: 10.6084/m9.figshare.21317475
title: Differentially expressed genes of O. niloticus F_brain-vs-M_brain

description: Differentially expressed genes between female and male brains of Nile tilapia
DOI: 10.6084/m9.figshare.12399236
title: Additional file 1 of Psychological status and behavior changes of the public during the COVID-19 epidemic in China

description: Additional file 1.
DOI: 10.6084/m9.figshare.8207501.v1
title: MOESM2 of LncRNA H19 regulates PI3Kâ Akt signal pathway by functioning as a ceRNA and predicts poor prognosis in colorectal cancer: integrative analysis of dysregulated ncRNA-associated ceRNA network

description: Additional file 2. The miRNAs and their target mRNAs in the ceRNA network.
DOI: 10.6084/m9.figshare.12926066
title: Additional file 10 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 10: Table S9. The SNP loci associated with yield-related traits have been detected via GWAS method in upland cotton.
DOI: 10.6084/m9.figshare.17120294.v1
title: Additional file 8 of Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

description: Additional file 8: Table S6. Cell wall-associated genes (PCC &gt; 0.8) used for co-expression network construction.
DOI: 10.6084/m9.figshare.12925985.v1
title: Additional file 3 of Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer

description: Additional file 3: Table S2. Potential protein-coding gene targets of KLF5 in CRC.
DOI: 10.6084/m9.figshare.12926087.v1
title: Additional file 5 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 5: Table S4. The significant SNPLDB loci associated with BN, BW and LP, respectively.
DOI: 10.6084/m9.figshare.12926090.v1
title: Additional file 6 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 6: Table S5. A total of 115 genes annotated in the six adjacent genome fragments of the stable SNPLDB loci.
DOI: 10.6084/m9.figshare.15020711.v1
title: Additional file 2 of Comparing the monetary value of a quality-adjusted life year from the payment card and the open-ended format

description: Additional file 2. Sensitive analysis of generalized linear models for WTP/QALY values. This is the result of sensitive analysis of GLMs.
DOI: 10.6084/m9.figshare.12926072.v1
title: Additional file 12 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 12: Table S11. The elastic GSC matrix and GSC eigenvectors.
DOI: 10.6084/m9.figshare.12925982
title: Additional file 2 of Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer

description: Additional file 2: Table S1. Potential lncRNA targets of KLF5 in CRC.
DOI: 10.6084/m9.figshare.17120405
title: Additional file 2 of Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

description: Additional file 2. Conserved and rewired miRNA-mRNA regulatory networks and hub miRNAs.
DOI: 10.6084/m9.figshare.12925982.v1
title: Additional file 2 of Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer

description: Additional file 2: Table S1. Potential lncRNA targets of KLF5 in CRC.
DOI: 10.6084/m9.figshare.12925985
title: Additional file 3 of Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer

description: Additional file 3: Table S2. Potential protein-coding gene targets of KLF5 in CRC.
DOI: 10.6084/m9.figshare.12926084.v1
title: Additional file 4 of An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

description: Additional file 4: Table S3. Analysis of variance of three yield-related traits in four planting environments.
DOI: 10.6084/m9.figshare.17120417
title: Additional file 4 of Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

description: Additional file 4. Enrichment analysis of the rewired miRNA-mRNA modules associated with miR-17/92 family.
DOI: 10.6084/m9.figshare.12399374
title: Additional file 2 of LIG4 syndrome: clinical and molecular characterization in a Chinese cohort

description: Additional file 2: Table S2. Clinical and immunophenotype comparison between genotypes p.R814X/p.K424Rfs*20 and p.R278/p.K424Rfs*20.
DOI: 10.5281/zenodo.10679005
title: Raw 4D-STEM tilt-series data of T4-bacteriophages

description: 4D-STEM tilt-series (tom1 and tom2) acquired using the SavvyScan system with ARINA/DECTRIS pixelated detector. 

Microscope settings: F20 transmission electron microscope, 200KV, microprobe 30u, SS9, gun5, 1.5nm/pix scan.

SerialEM settings: 1024X1024 probe locations per tilt view, dose-symmetric with group of 3, direction minus to plus, steps of 2 deg (tom1) and 3 deg (tom2).

File format:   [name of series]_s[tilt view number]_data_[file number].h5