cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5722192
title: Additional file 10: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: List of all TFs and expression of DEGs TFs in the 6 libraries. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.5722192.v1
title: Additional file 10: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: List of all TFs and expression of DEGs TFs in the 6 libraries. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.5722198
title: Additional file 11: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Expression and annotation of differentially expressed aux and SSEGs IME vs. ME. (XLSX 86 kb)
DOI: 10.6084/m9.figshare.5722198.v1
title: Additional file 11: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Expression and annotation of differentially expressed aux and SSEGs IME vs. ME. (XLSX 86 kb)
DOI: 10.6084/m9.figshare.5722234
title: Additional file 1: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Primers used in this study for qRT-PCR. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5722234.v1
title: Additional file 1: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Primers used in this study for qRT-PCR. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5722249
title: Additional file 2: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Lengths distribution of all assembled unigenes (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5722249.v1
title: Additional file 2: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Lengths distribution of all assembled unigenes (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5722264
title: Additional file 3: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Functional annotation of unigenes against Nr, Pfam, KEGG, COG, GO Swissprot databases. (XLS 20569 kb)
DOI: 10.6084/m9.figshare.5722264.v1
title: Additional file 3: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Functional annotation of unigenes against Nr, Pfam, KEGG, COG, GO Swissprot databases. (XLS 20569 kb)
DOI: 10.6084/m9.figshare.5722276
title: Additional file 4: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Gene ontology (GO) classification, COG classification and KEGG classification of unigenes. a. The GO terms are summarized into three main categories: biological process, cellular component and molecular function. b. COG classification of the unigenes. c. KEGG classification of 5933 KO annotated unigenes. (XLSX 111 kb)
DOI: 10.6084/m9.figshare.5722276.v1
title: Additional file 4: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Gene ontology (GO) classification, COG classification and KEGG classification of unigenes. a. The GO terms are summarized into three main categories: biological process, cellular component and molecular function. b. COG classification of the unigenes. c. KEGG classification of 5933 KO annotated unigenes. (XLSX 111 kb)
DOI: 10.6084/m9.figshare.5722285
title: Additional file 5: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Expression of genes in the 6 libraries in wheat callus based on the results of RNA-Seq. (XLSX 6574 kb)
DOI: 10.6084/m9.figshare.5722285.v1
title: Additional file 5: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Expression of genes in the 6 libraries in wheat callus based on the results of RNA-Seq. (XLSX 6574 kb)
DOI: 10.6084/m9.figshare.5722294
title: Additional file 6: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Information of DEGs in the comparisons of IME vs. ME. (XLSX 397 kb)
DOI: 10.6084/m9.figshare.5722294.v1
title: Additional file 6: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Information of DEGs in the comparisons of IME vs. ME. (XLSX 397 kb)
DOI: 10.6084/m9.figshare.5722303
title: Additional file 7: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Information of DEGs in the comparisons between stages in IMEs and MEs. (XLSX 319 kb)
DOI: 10.6084/m9.figshare.5722303.v1
title: Additional file 7: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Information of DEGs in the comparisons between stages in IMEs and MEs. (XLSX 319 kb)
DOI: 10.6084/m9.figshare.5722312
title: Additional file 8: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Functional annotation of all DEG against Nr, Pfam, Swissprot, KOG, KEGG, GO and COG databases. (XLSX 1510 kb)
DOI: 10.6084/m9.figshare.5722312.v1
title: Additional file 8: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: Functional annotation of all DEG against Nr, Pfam, Swissprot, KOG, KEGG, GO and COG databases. (XLSX 1510 kb)
DOI: 10.6084/m9.figshare.5722315
title: Additional file 9: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: KEGG enrichment analysis of all DEGs. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.5722315.v1
title: Additional file 9: of De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)

description: KEGG enrichment analysis of all DEGs. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.5725663
title: Data for Agent-Based Modeling of the interaction between CD8+ T cells and Beta cells in Type 1 Diabetes

description: This dataset contains data for the figures given in the following publication:<br>Agent-Based Modeling of the interaction between CD8+ T cells and Beta cells in Type 1 Diabetes<br><br>M. C. Ozturk, Q. Xu, and A. Cinar<br>PLoS ONE (2017) <br>DOI: http://dx.doi.org/10.1371/journal.pone.0190349
DOI: 10.6084/m9.figshare.5725663.v1
title: Data for Agent-Based Modeling of the interaction between CD8+ T cells and Beta cells in Type 1 Diabetes

description: This dataset contains data for the figures given in the following publication:<br>Agent-Based Modeling of the interaction between CD8+ T cells and Beta cells in Type 1 Diabetes<br><br>M. C. Ozturk, Q. Xu, and A. Cinar<br>PLoS ONE (2017) <br>DOI: http://dx.doi.org/10.1371/journal.pone.0190349
DOI: 10.6084/m9.figshare.5726155
title: Additional file 2: of Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

description: Excel table containing LungNet. (XLS 325 kb)
DOI: 10.6084/m9.figshare.5726155.v1
title: Additional file 2: of Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

description: Excel table containing LungNet. (XLS 325 kb)
DOI: 10.6084/m9.figshare.5726176
title: Additional file 3: of Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

description: Excel table containing the results of a GSEA on the target genes in LungNet. (XLS 242 kb)
DOI: 10.6084/m9.figshare.5726176.v1
title: Additional file 3: of Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

description: Excel table containing the results of a GSEA on the target genes in LungNet. (XLS 242 kb)
DOI: 10.6084/m9.figshare.5726185
title: Additional file 2 of Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders

description: Supplementary Tables. This file consists of long supplementary tables. (XLSX 13200 KB)
DOI: 10.6084/m9.figshare.5726185.v1
title: Additional file 2 of Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders

description: Supplementary Tables. This file consists of long supplementary tables. (XLSX 13200 KB)
DOI: 10.6084/m9.figshare.5726446
title: Additional file 1: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S1. Data used in the study. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5726446.v1
title: Additional file 1: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S1. Data used in the study. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5726497
title: Additional file 3: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S2. Cartilage-selective genes. (XLSX 45110 kb)
DOI: 10.6084/m9.figshare.5726497.v1
title: Additional file 3: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S2. Cartilage-selective genes. (XLSX 45110 kb)
DOI: 10.6084/m9.figshare.5726521
title: Additional file 4: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S3. Data comparison between microarray and RNA-seq platforms. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.5726521.v1
title: Additional file 4: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S3. Data comparison between microarray and RNA-seq platforms. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.5726533
title: Additional file 5: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S4. Cartilage-selective transcription factors and motif analysis. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.5726533.v1
title: Additional file 5: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S4. Cartilage-selective transcription factors and motif analysis. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.5726542
title: Additional file 6: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S5. GO analysis of cartilage-unique enhancers. (XLSX 1028 kb)
DOI: 10.6084/m9.figshare.5726542.v1
title: Additional file 6: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S5. GO analysis of cartilage-unique enhancers. (XLSX 1028 kb)
DOI: 10.6084/m9.figshare.5726560
title: Additional file 7: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S6. Cartilage selective lncRNAs. (XLSX 17845 kb)
DOI: 10.6084/m9.figshare.5726560.v1
title: Additional file 7: of Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

description: Supplementary Dataset S6. Cartilage selective lncRNAs. (XLSX 17845 kb)
DOI: 10.6084/m9.figshare.5726590
title: Additional file 3: of The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone

description: Microsatellite data file used for analyses. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.5726590.v1
title: Additional file 3: of The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone

description: Microsatellite data file used for analyses. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.5726608
title: MOESM2 of Metabolic regulations of a decoction of Hedyotis diffusa in acute liver injury of mouse models

description: Additional file 2. The up-regulated and down-regulated metabolites in different categories among control, LPS/GALN group and LPS/GALNÂ +Â HD group.
DOI: 10.6084/m9.figshare.5726608.v1
title: MOESM2 of Metabolic regulations of a decoction of Hedyotis diffusa in acute liver injury of mouse models

description: Additional file 2. The up-regulated and down-regulated metabolites in different categories among control, LPS/GALN group and LPS/GALNÂ +Â HD group.
DOI: 10.6084/m9.figshare.5727033
title: Negative impact of hyperglycaemia on mouse alveolar development

description: Diabetes mellitus in pregnancy has been known to affect the embryonic development of various systems, including cardiovascular and nervous systems. However, whether this disease could have a negative impact on embryonic respiratory system remains controversial. In this study, we demonstrated that pregestational diabetes mellitus (PGDM)-induced defects in lung development in mice are mainly characterized by the changes in the morphological structure of the lung. Immunostaining and Western blotting showed that proliferation increased and apoptosis decreased in PGDM. Hyperglycaemia caused pulmonary tissue fibrationas manifested by an increase in Masson staining and decorin expression in PGDM lungs, and the immunofluorescent pro-SPC<sup>+</sup> type II pulmonary epithelial cell number was decreased. The alteration of pulmonary epithelial cell differentiation might be due to hyperglycaemia-activated Wnt signalling and suppressed GATA6 expression in PGDM mouse lung tissues and MLE-12 cells. The treatment of MLE-12 cells with high glucose in the presence/absence of XAV939 or su5402 further proved that hyperglycaemia suppressed the expression of GATA6 and pro-SPC by activating Wnt signalling and induced the expression of decorin, α-SMA and TGF-β by activating Fgf signalling. Therefore, in this study, we revealed that hyperglycemia induced dysfunctional pulmonary cell apoptosis and proliferation, as well as pulmonary myofibroblast hyperplasia, which contributed to the formation of aberrant structure of alveolar walls. Furthermore, the hyperglycaemia also inhibited the differentiation of pulmonary epithelial cells through the canonical Wnt and Fgf signalling, and the alteration of Fgf and Wnt signalling activated TGF-β, which would promote the AECII EMT process.
DOI: 10.6084/m9.figshare.5727033.v1
title: Negative impact of hyperglycaemia on mouse alveolar development

description: Diabetes mellitus in pregnancy has been known to affect the embryonic development of various systems, including cardiovascular and nervous systems. However, whether this disease could have a negative impact on embryonic respiratory system remains controversial. In this study, we demonstrated that pregestational diabetes mellitus (PGDM)-induced defects in lung development in mice are mainly characterized by the changes in the morphological structure of the lung. Immunostaining and Western blotting showed that proliferation increased and apoptosis decreased in PGDM. Hyperglycaemia caused pulmonary tissue fibrationas manifested by an increase in Masson staining and decorin expression in PGDM lungs, and the immunofluorescent pro-SPC<sup>+</sup> type II pulmonary epithelial cell number was decreased. The alteration of pulmonary epithelial cell differentiation might be due to hyperglycaemia-activated Wnt signalling and suppressed GATA6 expression in PGDM mouse lung tissues and MLE-12 cells. The treatment of MLE-12 cells with high glucose in the presence/absence of XAV939 or su5402 further proved that hyperglycaemia suppressed the expression of GATA6 and pro-SPC by activating Wnt signalling and induced the expression of decorin, α-SMA and TGF-β by activating Fgf signalling. Therefore, in this study, we revealed that hyperglycemia induced dysfunctional pulmonary cell apoptosis and proliferation, as well as pulmonary myofibroblast hyperplasia, which contributed to the formation of aberrant structure of alveolar walls. Furthermore, the hyperglycaemia also inhibited the differentiation of pulmonary epithelial cells through the canonical Wnt and Fgf signalling, and the alteration of Fgf and Wnt signalling activated TGF-β, which would promote the AECII EMT process.
DOI: 10.6084/m9.figshare.5728596
title: Additional file 2: of Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics

description: The beak size data of 13 parids used in this study. (XLS 93Â kb)
DOI: 10.6084/m9.figshare.5728596.v1
title: Additional file 2: of Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics

description: The beak size data of 13 parids used in this study. (XLS 93Â kb)
DOI: 10.6084/m9.figshare.5728617
title: Additional file 3: of Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics

description: The beak shape data of 13 parids used in this study. (XLS 91Â kb)
DOI: 10.6084/m9.figshare.5728617.v1
title: Additional file 3: of Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics

description: The beak shape data of 13 parids used in this study. (XLS 91Â kb)
DOI: 10.6084/m9.figshare.5728635
title: Additional file 4: of Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics

description: The description of expression abundance of the 623 DEGs. (XLS 217Â kb)
DOI: 10.6084/m9.figshare.5728635.v1
title: Additional file 4: of Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics

description: The description of expression abundance of the 623 DEGs. (XLS 217Â kb)
DOI: 10.6084/m9.figshare.5728830
title: Additional file 1: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Expression data for Arabidopsis and rice MTase candidate genes of different development stage (XLSX 30 kb)
DOI: 10.6084/m9.figshare.5728830.v1
title: Additional file 1: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Expression data for Arabidopsis and rice MTase candidate genes of different development stage (XLSX 30 kb)
DOI: 10.6084/m9.figshare.5728842
title: Additional file 1: of Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism

description: An Excel file of all the detailed information. This Excel file includes four spreadsheets. These spreadsheets cover the following information:Spreadsheet 1: TCD-related organisms, organism IDs in NCBITaxon. Spreadsheet 2: Chemical components in TCDs, ChEBI IDs, and related references. Spreadsheet 3: TCD AEs including AE names, OAE AE IDs, related references. Spreadsheet 4: TCD-specific anatomic locations in organisms, and the PO and UBERON IDs corresponding to these anatomic entities. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.5728842.v1
title: Additional file 1: of Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism

description: An Excel file of all the detailed information. This Excel file includes four spreadsheets. These spreadsheets cover the following information:Spreadsheet 1: TCD-related organisms, organism IDs in NCBITaxon. Spreadsheet 2: Chemical components in TCDs, ChEBI IDs, and related references. Spreadsheet 3: TCD AEs including AE names, OAE AE IDs, related references. Spreadsheet 4: TCD-specific anatomic locations in organisms, and the PO and UBERON IDs corresponding to these anatomic entities. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.5728845
title: Additional file 2: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Expression data for Arabidopsis MTase candidate genes under various stress conditions (XLSX 24126 kb)
DOI: 10.6084/m9.figshare.5728845.v1
title: Additional file 2: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Expression data for Arabidopsis MTase candidate genes under various stress conditions (XLSX 24126 kb)
DOI: 10.6084/m9.figshare.5728866
title: Additional file 3: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Expression data for rice MTase candidate genes under stress conditions (XLSX 35573 kb)
DOI: 10.6084/m9.figshare.5728866.v1
title: Additional file 3: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Expression data for rice MTase candidate genes under stress conditions (XLSX 35573 kb)
DOI: 10.6084/m9.figshare.5728887
title: Additional file 4: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Protein sequences of MTase candidate genes from Arabidopsis or rice (XLSX 27 kb)
DOI: 10.6084/m9.figshare.5728887.v1
title: Additional file 4: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Protein sequences of MTase candidate genes from Arabidopsis or rice (XLSX 27 kb)
DOI: 10.6084/m9.figshare.5728908
title: Additional file 6: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Nucleoside abundance analysis for rice and Arabidopsis samples during stress or development (XLSX 30 kb)
DOI: 10.6084/m9.figshare.5728908.v1
title: Additional file 6: of Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis

description: Nucleoside abundance analysis for rice and Arabidopsis samples during stress or development (XLSX 30 kb)
DOI: 10.6084/m9.figshare.5728959
title: Additional file 2 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Full significant gene lists. This file lists all the significant genes detected by all five methods, each list in a separate worksheet. (XLSX 223 kb)
DOI: 10.6084/m9.figshare.5728959.v1
title: Additional file 2 of Super-delta: a new differential gene expression analysis procedure with robust data normalization

description: Full significant gene lists. This file lists all the significant genes detected by all five methods, each list in a separate worksheet. (XLSX 223 kb)