cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23609519.v1
title: m<sup>6</sup>A mRNA Methylation Analysis Provides Novel Insights into Pigmentation in Sheep Skin

description: N6-methyladenosine (m<sup>6</sup>A) is the most universal post-transcriptional modification of mRNA which may play important roles in verious species. However, the potential roles of m<sup>6</sup>A in the pigmentation of skin are not completely understood. To explore the role of m6A modification in pigmentation of sheep skin, we used MeRIP-seq and RNA-seq to profile the skin transcriptome in black and white coat color (<i>n=</i>3). Our results showed that an average of 7701 m<sup>6</sup>A peaks were obtained for all samples and the average length was 305.89 bp. The GGACUU sequence was the most enrichment motif and shared in black skin and white skin. The m<sup>6</sup>A peaks were mainly enriched in the CDS, 3'UTR and 5'UTR, especially in CDS region near the stop codon of the transcript. 235 signiﬁcantly differential peaks were found in black skin vs. white skin. The KEGG signaling pathways of downregulated and upregulated m<sup>6</sup>A peaks were mainly enriched in AGE-RAGE signaling pathway in diabetic complications, Viral carcinogenesis, Transcriptional misregulation in cancer, ABC transporters, Basal transcription factors and Thyroid hormone synthesis (<i>P</i> value &lt;0.05). For RNA-seq, 71 differently expressed genes (DEGs) were scanned in black skin vs. white skin. DEGs were significantly enriched in tyrosine metabolism, melanogenesis, neuroactive ligand-receptor interaction pathway (<i>P</i> value &lt;0.05). Combined m<sup>6</sup>A-seq and RNA-seq analysis showed that the hyper-up genes and hypo-up genes were both enriched in ErbB signaling pathway (<i>P</i> value &lt;0.05). In conclusion, it provide a basis for further research into the functions of m<sup>6</sup>A methylation modiﬁcations in pigmentation.
DOI: 10.6084/m9.figshare.12599391.v1
title: Additional file 1 of LcMYB4, an unknown function transcription factor gene from sheepgrass, as a positive regulator of chilling and freezing tolerance in transgenic Arabidopsis

description: Additional file 1: Table S1. All primers used in this study.
DOI: 10.6084/m9.figshare.13646893
title: Additional file 1 of Putative ligand binding sites of two functionally characterized bark beetle odorant receptors

description: Additional file 1: Supplementary Table 1. Annotation details of the Ips typographus odorant receptors (ORs), including names, amino acid sequences, expression levels, annotation notes, and correspondence with the original dataset [43].
DOI: 10.6084/m9.figshare.13646893.v1
title: Additional file 1 of Putative ligand binding sites of two functionally characterized bark beetle odorant receptors

description: Additional file 1: Supplementary Table 1. Annotation details of the Ips typographus odorant receptors (ORs), including names, amino acid sequences, expression levels, annotation notes, and correspondence with the original dataset [43].
DOI: 10.6084/m9.figshare.23084013
title: Additional file 1 of Whole genome sequencing and analysis of Armillaria gallica Jzi34 symbiotic with Gastrodia elata

description: Additional file 1: TableS1. Ka/Ks value for the collinear P450 gene pairs between A. gallica Jzi34 and other Armillaria.
DOI: 10.6084/m9.figshare.12599431.v1
title: Additional file 2 of Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

description: Additional file 2. Qualitative and quantitative of multi-omics data.
DOI: 10.6084/m9.figshare.12599437
title: Additional file 4 of Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

description: Additional file 4. Unsupervised time-resolved trend clustering analyses.
DOI: 10.6084/m9.figshare.12599440.v1
title: Additional file 5 of Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

description: Additional file 5. Proteins distributed in four different organelles.
DOI: 10.6084/m9.figshare.12599431
title: Additional file 2 of Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

description: Additional file 2. Qualitative and quantitative of multi-omics data.
DOI: 10.6084/m9.figshare.12599434
title: Additional file 3 of Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

description: Additional file 3. MEBA analysis for time-resolved metabolomics and proteomics datasets.
DOI: 10.6084/m9.figshare.12599455.v1
title: Additional file 3 of The I-MICRO trial, Ilomedin for treatment of septic shock with persistent microperfusion defects: a double-blind, randomized controlled trial—study protocol for a randomized controlled trial

description: Additional file 3:. SPIRIT 2013 Checklist: Recommended items to address in a clinical trial protocol and related documents.
DOI: 10.6084/m9.figshare.12599455
title: Additional file 3 of The I-MICRO trial, Ilomedin for treatment of septic shock with persistent microperfusion defects: a double-blind, randomized controlled trial—study protocol for a randomized controlled trial

description: Additional file 3:. SPIRIT 2013 Checklist: Recommended items to address in a clinical trial protocol and related documents.
DOI: 10.6084/m9.figshare.12599389
title: Additional file 1 of Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer

description: Additional file 1: Table S1. The NUMT/NUPT contents (contributed by organellar transcribed sequences) of desiccation-tolerant species and their controls. Table S2. The information used in assembling mitochondrial genomes. Table S3. The information used in assigning desiccation-tolerant species and their controls. Table S4. Genome information of the eukaryotes used in this study. Table S5. The NUMT/NUPT contents (contributed by organellar genomes) of desiccation-tolerant species and their controls.
DOI: 10.6084/m9.figshare.13646902
title: Additional file 4 of Putative ligand binding sites of two functionally characterized bark beetle odorant receptors

description: Additional file 4: Supplementary Data 2. Datasets from the HEK cell and oocyte assays conducted in this study as well as raw data from previous single sensillum recordings.
DOI: 10.6084/m9.figshare.9980258
title: MOESM10 of Study on cyanidin metabolism in petals of pink-flowered strawberry based on transcriptome sequencing and metabolite analysis

description: Additional file 10: Table S5. The numbers of differential expressed TFs related with ABP in the three development stages.
DOI: 10.6084/m9.figshare.9980258.v1
title: MOESM10 of Study on cyanidin metabolism in petals of pink-flowered strawberry based on transcriptome sequencing and metabolite analysis

description: Additional file 10: Table S5. The numbers of differential expressed TFs related with ABP in the three development stages.
DOI: 10.6084/m9.figshare.12599392.v1
title: Additional file 2 of Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer

description: Additional file 2: Data S1. The mitochondrial genome sequences assembled in this study.
DOI: 10.6084/m9.figshare.12599440
title: Additional file 5 of Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

description: Additional file 5. Proteins distributed in four different organelles.
DOI: 10.6084/m9.figshare.12599410.v1
title: Additional file 4 of Cow manure application effectively regulates the soil bacterial community in tea plantation

description: Additional file 4: Table S1. The relative abundance of the dominant phyla and P/A ratio in soil bacterial communities.
DOI: 10.6084/m9.figshare.12599533.v1
title: Additional file 4 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 4: Table S4. Significantly mutated genes in CRC patients with LM.
DOI: 10.6084/m9.figshare.12599434.v1
title: Additional file 3 of Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

description: Additional file 3. MEBA analysis for time-resolved metabolomics and proteomics datasets.
DOI: 10.6084/m9.figshare.9980369
title: MOESM2 of Transcriptional activation of CBFÎ˛ by CDK11p110 is necessary to promote osteosarcoma cell proliferation

description: Additional file 2: Table S1. Top 162 gene list analyzed by Genesifter.
DOI: 10.6084/m9.figshare.12599542.v1
title: Additional file 7 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 7: Table S6. Significant copy number gains and losses.
DOI: 10.6084/m9.figshare.9980369.v1
title: MOESM2 of Transcriptional activation of CBFÎ˛ by CDK11p110 is necessary to promote osteosarcoma cell proliferation

description: Additional file 2: Table S1. Top 162 gene list analyzed by Genesifter.
DOI: 10.6084/m9.figshare.9980372
title: MOESM3 of Transcriptional activation of CBFÎ˛ by CDK11p110 is necessary to promote osteosarcoma cell proliferation

description: Additional file 3: Table S2. Top 20 gene list analyzed by Qlucore.
DOI: 10.6084/m9.figshare.9980372.v1
title: MOESM3 of Transcriptional activation of CBFÎ˛ by CDK11p110 is necessary to promote osteosarcoma cell proliferation

description: Additional file 3: Table S2. Top 20 gene list analyzed by Qlucore.
DOI: 10.6084/m9.figshare.9980375
title: MOESM4 of Transcriptional activation of CBFÎ˛ by CDK11p110 is necessary to promote osteosarcoma cell proliferation

description: Additional file 4: Table S3. Characteristics of osteosarcoma patients and their tumor samples.
DOI: 10.6084/m9.figshare.9980375.v1
title: MOESM4 of Transcriptional activation of CBFÎ˛ by CDK11p110 is necessary to promote osteosarcoma cell proliferation

description: Additional file 4: Table S3. Characteristics of osteosarcoma patients and their tumor samples.
DOI: 10.6084/m9.figshare.12599530.v1
title: Additional file 3 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 3: Table S3. Summary of synonymous and nonsynonymous somatic mutations identified in the five CRC patients with LM.
DOI: 10.6084/m9.figshare.12599545
title: Additional file 8 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 8: Table S7. KEGG analysis of high-risk genes.
DOI: 10.6084/m9.figshare.9980381
title: MOESM10 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 10. Related to Fig. 5. SSVs associated with rearrangement of regions with high or low methylation. Using a dataset of DNA methylation of normal tissues, the average DNA methylation represented by the rearranged region (using window of 50 kb) was compared with that of the CGI nearby the gene on the other side of the SSV breakpoint, with the average difference in methylation beta values computed for all SSV-CGI associations, as well as for the subset of SSV-CGI associations involving higher or lower DNA methylation (defined using distance metric FDR &lt; 5% and methylation in cancer sample either &gt; 0.4SD or &lt; − 0.4SD from sample median for the case harboring the breakpoint).
DOI: 10.6084/m9.figshare.23084148
title: Additional file 3 of Extracellular arginine availability modulates eIF2α O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis

description: Additional file 3: Table S4. Proteomic raw data. Table S5. AS pathway
DOI: 10.6084/m9.figshare.9980381.v1
title: MOESM10 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 10. Related to Fig. 5. SSVs associated with rearrangement of regions with high or low methylation. Using a dataset of DNA methylation of normal tissues, the average DNA methylation represented by the rearranged region (using window of 50 kb) was compared with that of the CGI nearby the gene on the other side of the SSV breakpoint, with the average difference in methylation beta values computed for all SSV-CGI associations, as well as for the subset of SSV-CGI associations involving higher or lower DNA methylation (defined using distance metric FDR &lt; 5% and methylation in cancer sample either &gt; 0.4SD or &lt; − 0.4SD from sample median for the case harboring the breakpoint).
DOI: 10.6084/m9.figshare.12599533
title: Additional file 4 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 4: Table S4. Significantly mutated genes in CRC patients with LM.
DOI: 10.6084/m9.figshare.12599536.v1
title: Additional file 5 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 5: Table S5. Somatic copy number variation and affected genes.
DOI: 10.6084/m9.figshare.9980390
title: MOESM11 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 11. Related to Fig. 6. Complete set of molecular-level correlations with total number of SSV events detected across samples, according to regression model applied (i.e. what covariates were considered, all models including cancer type according to TCGA/ICGC project and high pass versus low pass WGS as covariates). DNA methylation and mRNA results are included in separate data tabs. Also includes Gene Ontology (GO) terms associated with genes positively correlated (FDRâ &lt;â 1%, with corrections for cancer type, CNA, and low pass versus high pass WGS) with the total number of SSV events.
DOI: 10.6084/m9.figshare.9980390.v1
title: MOESM11 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 11. Related to Fig. 6. Complete set of molecular-level correlations with total number of SSV events detected across samples, according to regression model applied (i.e. what covariates were considered, all models including cancer type according to TCGA/ICGC project and high pass versus low pass WGS as covariates). DNA methylation and mRNA results are included in separate data tabs. Also includes Gene Ontology (GO) terms associated with genes positively correlated (FDRâ &lt;â 1%, with corrections for cancer type, CNA, and low pass versus high pass WGS) with the total number of SSV events.
DOI: 10.6084/m9.figshare.13646902.v1
title: Additional file 4 of Putative ligand binding sites of two functionally characterized bark beetle odorant receptors

description: Additional file 4: Supplementary Data 2. Datasets from the HEK cell and oocyte assays conducted in this study as well as raw data from previous single sensillum recordings.
DOI: 10.6084/m9.figshare.12599536
title: Additional file 5 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 5: Table S5. Somatic copy number variation and affected genes.
DOI: 10.6084/m9.figshare.9980408
title: MOESM2 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 2. Related to Fig. 1. TCGA and ICGC cancer cases examined in this study.
DOI: 10.6084/m9.figshare.9980408.v1
title: MOESM2 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 2. Related to Fig. 1. TCGA and ICGC cancer cases examined in this study.
DOI: 10.6084/m9.figshare.9980411
title: MOESM3 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 3. Related to Fig. 1. SSV calls by Meerkat for 827 TCGA cases with high pass WGS data, for 761 of which RNA-seq data were available for analysis as part of the total combined set of 2334 cases.
DOI: 10.6084/m9.figshare.9980411.v1
title: MOESM3 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 3. Related to Fig. 1. SSV calls by Meerkat for 827 TCGA cases with high pass WGS data, for 761 of which RNA-seq data were available for analysis as part of the total combined set of 2334 cases.
DOI: 10.6084/m9.figshare.9980414
title: MOESM4 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 4. Related to Fig. 1. By genomic region windows method: complete set of gene-level correlations between expression and nearby SSV event, according to region examined (e.g. 0-20 kb upstream, 20-50 kb upstream, 50-100 kb upstream, 0-20 kb downstream, 20-50 kb downstream, 50-100 kb downstream, or within the gene body) and the regression model applied.
DOI: 10.6084/m9.figshare.9980414.v1
title: MOESM4 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 4. Related to Fig. 1. By genomic region windows method: complete set of gene-level correlations between expression and nearby SSV event, according to region examined (e.g. 0-20 kb upstream, 20-50 kb upstream, 50-100 kb upstream, 0-20 kb downstream, 20-50 kb downstream, 50-100 kb downstream, or within the gene body) and the regression model applied.
DOI: 10.6084/m9.figshare.9980417
title: MOESM5 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 5. Related to Fig. 2. By distance metric method: complete set of gene-level correlations between expression and nearby SSV event, according to regression model applied (i.e. what covariates were considered). The top significant mRNAs (FDRâ &lt;â 10%, correcting for cancer type and CNA) and related information are highlighted in a separate Excel tab. Results for microRNAs are provided in a separate Excel tab. Also includes Gene Ontology (GO) terms associated with genes positively correlated (FDRâ &lt;â 5%, with corrections for cancer type and CNA) with occurrence of SSV in proximity to the gene.
DOI: 10.6084/m9.figshare.12599586.v1
title: Additional file 1 of LcMYB4, an unknown function transcription factor gene from sheepgrass, as a positive regulator of chilling and freezing tolerance in transgenic Arabidopsis

description: Additional file 1: Table S1. All primers used in this study.
DOI: 10.6084/m9.figshare.6832412.v1
title: New age determinations for the Banhadão and Itapirapuã complexes in the Ribeira Valley, southern Brazil

description: ABSTRACT: New age determinations by Ar-Ar and U-Pb SHRIMP for the alkaline complexes of Banhadão and Itapirapuã that occur in the Ribeira Valley are in agreement with the previously radiometric K-Ar ages available in literature. Ar-Ar ages on biotite for Banhadão range in the 106-110 Ma interval, and suggest a minimum age of 106 Ma for the complex. Ar-Ar data on biotite for Itapirapuã are more uniform, indicating an age of 102 Ma for the complex. U-Pb SHRIMP determinations on titanite from Itapirapuã melanite syenitic rocks yielded an age of ~106 Ma. Thus, the age interval of 100 and 110 Ma does exist indeed, suggesting an intermediate magmatic pulse between the already well-defined peaks of 80-90 Ma and 130-140 Ma for the alkaline rocks in southern Brazil, confirming the periodicity of the magmatism.
DOI: 10.6084/m9.figshare.9980417.v1
title: MOESM5 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 5. Related to Fig. 2. By distance metric method: complete set of gene-level correlations between expression and nearby SSV event, according to regression model applied (i.e. what covariates were considered). The top significant mRNAs (FDRâ &lt;â 10%, correcting for cancer type and CNA) and related information are highlighted in a separate Excel tab. Results for microRNAs are provided in a separate Excel tab. Also includes Gene Ontology (GO) terms associated with genes positively correlated (FDRâ &lt;â 5%, with corrections for cancer type and CNA) with occurrence of SSV in proximity to the gene.
DOI: 10.6084/m9.figshare.12599542
title: Additional file 7 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 7: Table S6. Significant copy number gains and losses.
DOI: 10.6084/m9.figshare.12599586
title: Additional file 1 of LcMYB4, an unknown function transcription factor gene from sheepgrass, as a positive regulator of chilling and freezing tolerance in transgenic Arabidopsis

description: Additional file 1: Table S1. All primers used in this study.
DOI: 10.6084/m9.figshare.24136194
title: <b>The protective effect of Artesunate on diabetic retinopathy through lncRNA HOTAIR/miR-106a-5p/VEGF pathway</b>

description: The rat Diabetic retinopathy (DR) model was established with streptozotocin, and Art treatment was given. During induction, fasting blood glucose (FBG) levels were measured weekly; H&E staining was used to observe the histological morphology of the retina; HbA1c levels and TNF-α, IL-1β, MDA, GPx levels in rat serum and tissues were detected by ELISA; Claudin-5, Occludin and ZO-1 levels in tissues were detected by qRT-PCR. High glucose or Art was used to culture human retinal microvascular endothelial cells (HRCECs). MTT, flow cytometry, and tube formation experiments were used to detect cell proliferation, apoptosis, and tube formation ability. qRT-PCR was used to detect lncRNA HOTAIR, miR-106a -5p, and VEGF expression; a Dual-Luciferase reporter gene experiment was used to verify the targeting relationship between miR-106a-5p and HOTAIR or VEGF. Western blot was used to detect the protein expression of GFAP, HIF-1α, and VEGF in tissues or cells.
DOI: 10.6084/m9.figshare.12599545.v1
title: Additional file 8 of Genomic profiling of colorectal cancer with isolated lung metastasis

description: Additional file 8: Table S7. KEGG analysis of high-risk genes.
DOI: 10.6084/m9.figshare.9980420
title: MOESM6 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 6. Related to Fig. 3. By distance metric method: complete set of gene-level correlations between expression and nearby SSV event for each individual cancer type (using regression model with corrections for cancer type and CNA). Data for the 893 CGI DNA methylation probes showing both high cancer type-specific methylation and significant positive correlation between expression and SSV breakpoint for any one of the 20 cancer types surveyed (from Fig. 3d) are in a separate data tab.
DOI: 10.6084/m9.figshare.12599598
title: Additional file 5 of LcMYB4, an unknown function transcription factor gene from sheepgrass, as a positive regulator of chilling and freezing tolerance in transgenic Arabidopsis

description: Additional file 5: Table S2. LcMYB4 binding proteins in sheegrass seedling
DOI: 10.6084/m9.figshare.9980420.v1
title: MOESM6 of Global impact of somatic structural variation on the DNA methylome of human cancers

description: Additional file 6. Related to Fig. 3. By distance metric method: complete set of gene-level correlations between expression and nearby SSV event for each individual cancer type (using regression model with corrections for cancer type and CNA). Data for the 893 CGI DNA methylation probes showing both high cancer type-specific methylation and significant positive correlation between expression and SSV breakpoint for any one of the 20 cancer types surveyed (from Fig. 3d) are in a separate data tab.