cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.7u77kr
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polyalthia tipuliflora D.M.Johnson"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075428-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hfr33e
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllocosmus calothyrsus Mildbr."
 ]
}

 The dataset includes 110 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075429-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qhgrdd
title: Occurrence Download

description: A dataset containing 248 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phoebe neuranthoides S.K.Lee & F.N.Wei"
 ]
}

 The dataset includes 248 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075430-240321170329656/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.13265787
title: Additional file 7 of Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)

description: Additional file 7: Table S2. GO annotations of 43 differential genes used for WGCNA analysis
DOI: 10.6084/m9.figshare.7502876.v1
title: Additional file 10: of High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

description: Table S6. The results of alignment between the genetic map and the reference genome. (XLSX 121 kb)
DOI: 10.6084/m9.figshare.4363907
title: Additional file 2 of China’s conversion of cropland to forest program: a systematic review of the environmental and socioeconomic effects

description: Additional file 2: Full bibliographies and data extraction of included studies.
DOI: 10.6084/m9.figshare.14843199.v1
title: Additional file 1 of VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments

description: Additional file 1. VISPR-online source code and sample data. Code and sample data used for test.
DOI: 10.6084/m9.figshare.7502885
title: Additional file 12: of High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

description: Table S7. The marker annotation of the genetic map. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7503107.v1
title: Additional file 2: of Comparative RNA-sequencing-based transcriptome profiling of buds from profusely flowering ‘Qinguan’ and weakly flowering ‘Nagafu no. 2’ apple varieties reveals novel insights into the regulatory mechanisms underlying floral induction

description: Table S4. Kyoto Encyclopedia of Genes and Genomes analysis of up-regulated genes, including the seven expression pattern types (a-, b-, c-, d-, e-, f-, and g-type) in ‘Qinguan’ buds relative to ‘Nagafu No. 2’ buds. The up-regulated genes were identified based on the Venn diagrams and cluster analysis in Fig. 5. Table S5. Kyoto Encyclopedia of Genes and Genomes analysis of down-regulated genes, including the seven expression pattern types (a-, b-, c-, d-, e-, f-, and g-type) in ‘Qinguan’ buds relative to ‘Nagafu No. 2’ buds. The down-regulated genes were identified based on the Venn diagrams and cluster analysis in Fig. 5. Table S6. Carbohydrate, fatty acid, and lipid pathways related to differentially expressed genes in ‘Qinguan’ and ‘Nagafu No. 2’ buds. The differentially expressed genes were detected based on the model in Fig. 7. Table S7. Hormone pathways related to differentially expressed genes in ‘Qinguan’ and ‘Nagafu No. 2’ buds. These hormone-related genes are mainly involved in hormone synthesis, signaling, and response pathways. The model and cluster analysis of these genes are presented in Figs. 8 and 9. Table S8. Detailed information of transcription factor family members in ‘Qinguan’ and ‘Nagafu No. 2’ buds. Table S9. Differentially expressed flowering-related genes in ‘Qinguan’ and ‘Nagafu No. 2’ buds. The flowering-related genes located on different chromosomes are presented in Fig. 11. (XLSX 153 kb)
DOI: 10.6084/m9.figshare.7502891
title: Additional file 1: of High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

description: Table S1. The statistics of sequencing results (the adaptors consisted of recognition base and overhang). (XLSX 34 kb)
DOI: 10.6084/m9.figshare.13265763.v1
title: Additional file 10 of Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)

description: Additional file 10: Table S5. RT-PCR primer list.
DOI: 10.6084/m9.figshare.7502891.v1
title: Additional file 1: of High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

description: Table S1. The statistics of sequencing results (the adaptors consisted of recognition base and overhang). (XLSX 34 kb)
DOI: 10.6084/m9.figshare.8034134
title: 1000 Genome genotype

description: The 1000 Genome genotype used in the study
DOI: 10.6084/m9.figshare.6461405.v1
title: Additional file 11: of A newly formed hexaploid wheat exhibits immediate higher tolerance to nitrogen-deficiency than its parental lines

description: Table S2. Primers for q-RT-PCR analysis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7502951
title: Additional file 8: of High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

description: Figure S2. A comparison of current and previous genetic maps (map 1 is our SNP genetic map, map 2 quoted from previous study). (ZIP 210362 kb)
DOI: 10.6084/m9.figshare.20086055
title: Additional file 1 of Genetic diversity and population structure of Caryopteris mongholica revealed by reduced representation sequencing

description: Additional file 1: Table S1. List of 125 C. mongholica individuals tested in this study. Table S2. Summary of GBS data. Table S3. Environmental parameters used in this study, and the mean (±standard deviation) values of 18 locations. Table S4. 17 bioclimatic variables in the 18 locations of C. mongholica
DOI: 10.6084/m9.figshare.13265766
title: Additional file 11 of Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)

description: Additional file 11: Table S6. The pearson correlation analysis between RNASeq and qRT-PCR data.
DOI: 10.6084/m9.figshare.13265784
title: Additional file 6 of Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)

description: Additional file 6: Table S1. RNA sequencing data and corresponding quality control.
DOI: 10.6084/m9.figshare.13265790
title: Additional file 8 of Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)

description: Additional file 8: Table S3. KEGG annotations of 43 differential genes used for WGCNA analysis
DOI: 10.6084/m9.figshare.7503008
title: Additional file 1: of GJA1 (connexin43) is a key regulator of Alzheimer’s disease pathogenesis

description: Tables S1. Clinical and pathological traits, brain regions analyzed by transcriptome profiling, and sample classification with respect to the severity stage of each trait. Table S2. Correlations between GJA1 expression and individual phenotypical traits. Table S3. Differential expression analysis. TableS4. Covariables' impacts on GJA1 association with AD traits. Table S5. Gene ontology analysis. Table S6. Intersection of GJA1 gene signatures and AD gene signatures. Table S7. Intersection of GJA1 gene signatures and the khiki module. Table S8. GJA1_centered genetic network analysis. Table S9A. GJA1 DEG signatures (AST+NEU) overlapped with brain cell type specific gene signatures. Table S9B. AST+NEU vs AST in Gja1 (-/-) or (+/+) DEG signatures overlapped with brain cell type specific gene signatures. Table S9C. differentially expressed genes in neurons upon GJA1 KO or not in astrocyte and neuron coculture. Table S9D. Difference of change degree in AST+NEU_vs_AST_Gja1(-/-) vs AST+NEU_vs_AST_Gja1(+/+). Table S10. List of primer sets and Universal Probe Library (UPL) probe for qRT-PCR. (XLSX 234 kb)
DOI: 10.6084/m9.figshare.7503020
title: Additional file 1: of Integrating proteomic and phosphoproteomic data for pathway analysis in breast cancer

description: Table S1. The results of different pathway ranking methods. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.22714860
title: Alkannin reverses lipopolysaccharides-induced inflammatory responses by suppressing mitogen-activated protein kinase and nuclear factor kappa-B signalling

description: Rheumatoid arthritis (RA) is an inflammatory disease that seriously affects human health worldwide. Meanwhile, inflammation in RAW264.7 cells could lead to the progression of RA. Alkannin (ALK) is derived from <i>Alkanna tinctoria</i> and is known to exert anti-tumor effects. However, the function of ALK in inflammation of RAW264.7 cells remains unclear. Thus, this research sought to investigate the detailed function of ALK in inflammatory responses of RAW264.7 cells. To induce an inflammatory response, RAW264.7 cells were exposed to lipopolysaccharide (LPS). MTT assay was applied to examine cell viability. Enzyme-linked immunosorbent assay (ELISA) was used to assess the levels of inflammatory cytokines. Furthermore, the mechanism underlying ALK function in inflammatory responses was investigated using RT-qPCR and western blotting. The data revealed that LPS significantly increased the expression of cyclooxygenase 2 (COX-2), Interleukin (IL)-1β, inducible nitric oxide synthase (iNOS), tumor necrosis factor-α (TNF-α), and IL-6, whereas ALK reversed this effect. ALK also restored LPS-induced nuclear factor kappa-B (NF-κB) activation by inhibiting the downregulation of p-inhibitor kappa B alpha (IκBα). LPS elevated p-extracellular regulated protein kinases 1/2 (ERK1/2), phosphorylated p38 (p-p38), and phosphorylated -c-Jun N-terminal kinase (p-JNK) levels, which were markedly decreased in the presence of ALK. In summary, Alkannin attenuated LPS-induced inflammation by inhibiting NF-κB and MAPK signaling. Thus, our research might provide a new theoretical basis for exploring new strategies against RA.
DOI: 10.6084/m9.figshare.22714860.v1
title: Alkannin reverses lipopolysaccharides-induced inflammatory responses by suppressing mitogen-activated protein kinase and nuclear factor kappa-B signalling

description: Rheumatoid arthritis (RA) is an inflammatory disease that seriously affects human health worldwide. Meanwhile, inflammation in RAW264.7 cells could lead to the progression of RA. Alkannin (ALK) is derived from <i>Alkanna tinctoria</i> and is known to exert anti-tumor effects. However, the function of ALK in inflammation of RAW264.7 cells remains unclear. Thus, this research sought to investigate the detailed function of ALK in inflammatory responses of RAW264.7 cells. To induce an inflammatory response, RAW264.7 cells were exposed to lipopolysaccharide (LPS). MTT assay was applied to examine cell viability. Enzyme-linked immunosorbent assay (ELISA) was used to assess the levels of inflammatory cytokines. Furthermore, the mechanism underlying ALK function in inflammatory responses was investigated using RT-qPCR and western blotting. The data revealed that LPS significantly increased the expression of cyclooxygenase 2 (COX-2), Interleukin (IL)-1β, inducible nitric oxide synthase (iNOS), tumor necrosis factor-α (TNF-α), and IL-6, whereas ALK reversed this effect. ALK also restored LPS-induced nuclear factor kappa-B (NF-κB) activation by inhibiting the downregulation of p-inhibitor kappa B alpha (IκBα). LPS elevated p-extracellular regulated protein kinases 1/2 (ERK1/2), phosphorylated p38 (p-p38), and phosphorylated -c-Jun N-terminal kinase (p-JNK) levels, which were markedly decreased in the presence of ALK. In summary, Alkannin attenuated LPS-induced inflammation by inhibiting NF-κB and MAPK signaling. Thus, our research might provide a new theoretical basis for exploring new strategies against RA.
DOI: 10.6084/m9.figshare.14843224
title: Additional file 8 of Genome-wide identification of Brassicaceae B-BOX genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed

description: Additional file 8: Table S1. Information about identified BBX genes. Table S2. Synteny analysis of Brassicaceae BBX genes. Table S3. Synteny analysis of Arabidopsis and each other Brassicaceae BBX genes. Table S4. Common DEGs in root among different classes. Table S5. Common DEGs in root among different classes.
DOI: 10.6084/m9.figshare.20086052
title: Additional file 1 of The study of direct and indirect effects of radiofrequency ablation on tumor microenvironment in liver tumor animal model

description: Additional file 1.
DOI: 10.6084/m9.figshare.14843224.v1
title: Additional file 8 of Genome-wide identification of Brassicaceae B-BOX genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed

description: Additional file 8: Table S1. Information about identified BBX genes. Table S2. Synteny analysis of Brassicaceae BBX genes. Table S3. Synteny analysis of Arabidopsis and each other Brassicaceae BBX genes. Table S4. Common DEGs in root among different classes. Table S5. Common DEGs in root among different classes.
DOI: 10.6084/m9.figshare.20086055.v1
title: Additional file 1 of Genetic diversity and population structure of Caryopteris mongholica revealed by reduced representation sequencing

description: Additional file 1: Table S1. List of 125 C. mongholica individuals tested in this study. Table S2. Summary of GBS data. Table S3. Environmental parameters used in this study, and the mean (±standard deviation) values of 18 locations. Table S4. 17 bioclimatic variables in the 18 locations of C. mongholica
DOI: 10.6084/m9.figshare.16940341.v1
title: Knockdown of circular RNA septin 9 inhibits the malignant progression of breast cancer by reducing the expression of solute carrier family 1 member 5 in a microRNA-149-5p-dependent manner

description: Breast cancer (BC) is the most frequently diagnosed cancer in women. Increasing evidence suggests that circular RNA (circRNA) exerts critical functions in BC progression. However, the roles of circRNA septin 9 (circSEPT9) in BC development and the underneath mechanism remain largely unclear so far. In this work, the RNA levels of circSEPT9, microRNA-149-5p (miR-149-5p) and solute carrier family 1 member 5 (SLC1A5) were detected by quantitative real-time polymerase chain reaction. Western blot was performed to check protein expression. Glutamine uptake, cell proliferation and cell apoptosis were investigated by glutamine uptake, cell counting kit-8, cell colony formation, 5-Ethynyl-29-deoxyuridine, flow cytometry analysis or DNA content quantitation assay. The interactions of miR-149-5p with circSEPT9 and SLC1A5 were identified by a dual-luciferase reporter assay. Mouse model assay was carried out to analyze the effect of circSEPT9 on tumor formation <i>in vivo</i>. Results showed that circSEPT9 and SLC1A5 expression were significantly upregulated, while miR-149-5p was downregulated in BC tissues and cells as compared with paracancerous normal breast tissues and human normal breast cells. Knockdown of circSEPT9 or SLC1A5 inhibited glutamine uptake and cell proliferation, but induced cell apoptosis in BC cells. SLC1A5 overexpression relieved circSEPT9 silencing-induced repression of BC cell malignancy. In mechanism, circSEPT9 regulated SLC1A5 expression by sponging miR-149-5p. In support, circSEPT9 knockdown led to delayed tumor tumorigenesis <i>in vivo</i>. In summary, these results indicates that circSEPT9 may act an oncogenic role in BC malignant progression by regulating miR-149-5p/SLC1A5 pathway, providing a novel mechanism responsible for BC development.
DOI: 10.6084/m9.figshare.14843175.v1
title: Additional file 2 of The dynamics of N6-methyladenine RNA modification in interactions between rice and plant viruses

description: Additional file 2: Table S1. Primers used for RSV and RBSDV detections in this study. Table S2. Sequenced and rice genome mapped reads in m6A-IP-seq, input RNA-seq rice samples. Table S3. Nucleotide localization and enrichment of the top 10 m6A peaks identified in Mock-, RSV-, and RBSDV-infected rice transcripts by m6A-IP-Seq. Table S4. The category of the differential m6A peaks upon two viruses' infection in rice. Table S5. Nucleotide localization and enrichment of the m6A peaks identified in RSV and RBSDV genomics by m6A-IP-Seq. Table S6. Gene ID and their fpkm analyses. Table S7. Different peaks statistic. Table S8. The m6A peaks appeared in different treatments. Table S9. The most abundant consensus motif in Mock, RSV-, and RBSDV-infected rice plant using suite of DREME and MEME. Table S10. Analyses of the m6A peaks that containing most four common consensus appeared in other species. Table S11. Detail information of ListHits Gene and m6A methylated genes under rice viruses’ infection derived from Additional file 2: Table S16. Table S12. Integrated analyses of the m6A methylation related genes with m6A modifications and expression profiles. Table S13. Integrated analyses of the anti-viral RNA silencing pathway related genes with m6A modification and expression profile. Table S14. Integrated analyses of the plant hormone metabolic genes with m6A modifications and expression profiles. Table S15. Integrated analyses of the relationship betwwen relative expression and m6A positions. Table S16. Summary of the m6A RNA methylation level in enriched top 5 KEGG pathways related genes from RNA-seq under rice viruses’ infection. Table S17. Detail information of the common m6A methylated genes appeared in enriched top 5 KEGG pathways under rice viruses' infection. Table S18. Primers used for qRT-PCR validation of the methylation of OsAGO18 and OsSLRL1 genes. Table S19. Primers used in qRT-PCR qualification of the candidate genes.
DOI: 10.6084/m9.figshare.14843199
title: Additional file 1 of VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments

description: Additional file 1. VISPR-online source code and sample data. Code and sample data used for test.
DOI: 10.7488/ds/7681
title: MG1655-T7 Single Cell Infection Videos and Segmentation

description: This dataset contains videos of single MG1655 E. coli cells infected by T7 bacteriophage. The results of the study are present in the doctoral thesis "A Single-Cell Study of the Biophysics of Bacteriophage Infection" by the dataset author. Segmentation of the videos is done via DeLTA2.0. Two python scripts with example code for visualisation of the data are provided for the downloader's benefit.
DOI: 10.6084/m9.figshare.14843254.v1
title: Additional file 3 of Evolutionary analysis and functional characterization of SiBRI1 as a Brassinosteroid receptor gene in foxtail millet

description: Additional file 3.
DOI: 10.34740/kaggle/dsv/7613337
title: Data Science Freelancer Listings:Upwork Dataset 📊
DOI: 10.6084/m9.figshare.14843254
title: Additional file 3 of Evolutionary analysis and functional characterization of SiBRI1 as a Brassinosteroid receptor gene in foxtail millet

description: Additional file 3.
DOI: 10.6084/m9.figshare.12746150
title: OxCOVID19 Database: a multimodal data repository for better understanding the global impact of Covid-19

description: These files contain a snapshot of the database described
in <strong>MANUSCRIPT</strong>* as of <strong>31-07-2020</strong>. The schema.org file contains a plain text description of the tables. The tables themselves are in the CSV files. The covid19db-figshare-master.zip contains the schemas along the scripts that where used to download these data and some example usage. A complete
listing of the variables and their sources can be found in <strong>MANUSCRIPT</strong>. <br><br>Since the OxCOVID19
Database draws from multiple data sources there are different licenses for
different tables, please see https://covid19.eng.ox.ac.uk/ for additional
details.<br><br>* The manuscript is currently under consideration, this description of the data will be updated when there is a publicly available version. In the meantime, please refer to https://covid19.eng.ox.ac.uk/
DOI: 10.6084/m9.figshare.14843356.v1
title: Additional file 8 of Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

description: Additional file 8: GO analysis of up-and down- regulated DE-circRNAs (whose host genes are DEGs) in the fetus vs. child (sheet 1 and 2) and fetus vs. adult (sheet 3 and 4) groups.
DOI: 10.34740/kaggle/ds/4433530
title: Data Science Freelancer Listings:Upwork Dataset 📊
DOI: 10.6084/m9.figshare.14843350.v1
title: Additional file 6 of Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

description: Additional file 6: P-adj of all DE-circRNAs (sheet 1) and DEGs (sheet 2).
DOI: 10.6084/m9.figshare.14843329.v1
title: Additional file 10 of Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

description: Additional file 10: miRNAs with DE-circRNA binding sites.
DOI: 10.6084/m9.figshare.14843295
title: Additional file 8 of Downstream of GA4, PbCYP78A6 participates in regulating cell cycle-related genes and parthenogenesis in pear (Pyrus bretshneideri Rehd.)

description: Additional file 8: Supplementary Table S3. List of qRT-PCR primers.
DOI: 10.6084/m9.figshare.14843344
title: Additional file 4 of Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

description: Additional file 4: Data overview of all libraries.
DOI: 10.6084/m9.figshare.14843295.v1
title: Additional file 8 of Downstream of GA4, PbCYP78A6 participates in regulating cell cycle-related genes and parthenogenesis in pear (Pyrus bretshneideri Rehd.)

description: Additional file 8: Supplementary Table S3. List of qRT-PCR primers.
DOI: 10.6084/m9.figshare.14843298
title: Additional file 9 of Downstream of GA4, PbCYP78A6 participates in regulating cell cycle-related genes and parthenogenesis in pear (Pyrus bretshneideri Rehd.)

description: Additional file 9: Supplementary Table S4. List of primers cloning PbCYP78A6-like.
DOI: 10.6084/m9.figshare.14843344.v1
title: Additional file 4 of Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

description: Additional file 4: Data overview of all libraries.
DOI: 10.6084/m9.figshare.14843298.v1
title: Additional file 9 of Downstream of GA4, PbCYP78A6 participates in regulating cell cycle-related genes and parthenogenesis in pear (Pyrus bretshneideri Rehd.)

description: Additional file 9: Supplementary Table S4. List of primers cloning PbCYP78A6-like.
DOI: 10.6084/m9.figshare.14843350
title: Additional file 6 of Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

description: Additional file 6: P-adj of all DE-circRNAs (sheet 1) and DEGs (sheet 2).
DOI: 10.6084/m9.figshare.14843356
title: Additional file 8 of Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

description: Additional file 8: GO analysis of up-and down- regulated DE-circRNAs (whose host genes are DEGs) in the fetus vs. child (sheet 1 and 2) and fetus vs. adult (sheet 3 and 4) groups.