cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12324851
title: Additional file 4 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S3. Structurally variable regions between neighboring stages and hot structurally variable regions.
DOI: 10.6084/m9.figshare.12324854
title: Additional file 5 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S4. Results of motif enrichment analysis in 3′ UTR structurally variable regions.
DOI: 10.6084/m9.figshare.12324857
title: Additional file 6 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S5. Summary of DLE element in structurally variable regions during early development and its associated biological function.
DOI: 10.6084/m9.figshare.7081898
title: Additional file 1: of Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration

description: List of primers used for qPCR in this study. 18S RNA was used as an internal control. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7082069
title: Additional file 8: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

description: Table S7. Differentially expressed transcripts in common from the rice microarray and RNA-Seq data analyses. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7082096
title: Additional file 11: of LGR5, a novel functional glioma stem cell marker, promotes EMT by activating the Wnt/Î˛-catenin pathway and predicts poor survival of glioma patients

description: Table S4. Univariate analysis of factors associated with prognosis in the LGG group. (XLS 12 kb)
DOI: 10.6084/m9.figshare.7082168
title: Additional file 9: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S6. Differentially enriched GMMs: The relative abundance and statistical test of the GMMs. (XLS 394 kb)
DOI: 10.6084/m9.figshare.12324845.v1
title: Additional file 2 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S1. Summary and statistics of icSHAPE, RNA-seq and iCLIP.
DOI: 10.6084/m9.figshare.12324851.v1
title: Additional file 4 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S3. Structurally variable regions between neighboring stages and hot structurally variable regions.
DOI: 10.6084/m9.figshare.7081901.v1
title: Additional file 9: of Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing

description: Table S7. CircRNAs with protein-coding potential. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.7081997
title: Additional file 4: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

description: Table S3. The putative transcription factors encoded by the rice genes under the control of PIPs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7082105
title: Additional file 1: of LGR5, a novel functional glioma stem cell marker, promotes EMT by activating the Wnt/Î˛-catenin pathway and predicts poor survival of glioma patients

description: Table S1. Association of LGR5 expression with clinicopathological features in HGG group. (XLS 10 kb)
DOI: 10.6084/m9.figshare.7082105.v1
title: Additional file 1: of LGR5, a novel functional glioma stem cell marker, promotes EMT by activating the Wnt/Î˛-catenin pathway and predicts poor survival of glioma patients

description: Table S1. Association of LGR5 expression with clinicopathological features in HGG group. (XLS 10 kb)
DOI: 10.6084/m9.figshare.7082114
title: Additional file 2: of LGR5, a novel functional glioma stem cell marker, promotes EMT by activating the Wnt/Î˛-catenin pathway and predicts poor survival of glioma patients

description: Table S2. Association of LGR5 expression with clinicopathological features in LGG group. (XLS 10 kb)
DOI: 10.6084/m9.figshare.7081997.v1
title: Additional file 4: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

description: Table S3. The putative transcription factors encoded by the rice genes under the control of PIPs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7082120
title: Additional file 6: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S4. The phylum: The relative abundance and statistical test of the phylum. (XLS 95 kb)
DOI: 10.6084/m9.figshare.7082144
title: Additional file 8: of Nogo-B receptor increases the resistance to tamoxifen in estrogen receptor-positive breast cancer cells

description: Survivin (BIRC5) mRNA expression data were retrieved from a gene-expression profiling dataset (202094_x from Kaplan–Meier Plot database) of 2046 patients with ERα-positive breast cancer and 928 patients with ERα-positive breast cancer treated with endocrine therapy. Kaplan–Meier analysis revealed significantly reduced relapse-free survival (RFS) (p &lt; 0.05) in 1023 patients with ERα-positive breast cancer with high survivin expression in tumors as compared to 1023 patients with low survivin expression in tumors. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.12324812.v1
title: Additional file 1 of Elucidating the roles of three β-glucuronosyltransferases (GLCATs) acting on arabinogalactan-proteins using a CRISPR-Cas9 multiplexing approach in Arabidopsis

description: Additional file 1: Five supplemental tables, three supplemental figures and their corresponding legends. Table S1. List of guide RNA sequences and their target genes. Table S2. List of primers used to assemble three gRNAs (A1, B1, and C1) into pHEE401E binary vector. Table S3. List of primers used to assemble four gRNAs (A2, B1, C2, and C3) into pHEE401E binary vector. Table S4. List of primers for sequencing off-targets. Table S5. List of primers used for qRT-PCR. Figure S1. Amino acid sequence alignment of GLCAT14A, GLCAT14B, and GLCAT14C. Figure S2. Expression profiles of GLCAT14A, GLCAT14B, and GLCAT14C obtained from the Klepikova Arabidopsis Atlas eFP Browser of the Bio-Analytic Resource for Plant Biology (BAR) [18]. The link for the expression profile of GLCAT14A can be found at http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?primaryGene=AT5G39990&dataSource=Klepikova_Atlas&modeInput=Absolute; The link for the expression profile of GLCAT14B can be found at http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?primaryGene=AT5G15050&dataSource=Klepikova_Atlas&modeInput=Absolute; The link for the expression profile of GLCAT14C can be found at http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?primaryGene=AT2G37585&dataSource=Klepikova_Atlas&modeInput=Absolute. Figure S3. Expression patterns of GLCAT14A, GLCAT14B, and GLCAT14C during seed development obtained from the Arabidopsis eFP Browser of the Bio-Analytic Resource for Plant Biology (BAR) (bar.utoronto.ca). The link for the expression profile of GLCAT14A during seed development can be found at http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=Seed&modeInput=Absolute&primaryGene=At5g39990&secondaryGene=At3g27340&override=None&threshold=219.05&modeMask_low=None&modeMask_stddev=None; The link for the expression profile of GLCAT14B during seed development can be found at http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=Seed&modeInput=Absolute&primaryGene=AT5G15050&secondaryGene=At3g27340&override=&threshold=17.75&modeMask_low=None&modeMask_stddev=None&gene_alias1=GlcAT14B&gene_alias2=; The link for the expression profile of GLCAT14C during seed development can be found at http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi?dataSource=Seed&modeInput=Absolute&primaryGene=AT2G37585&secondaryGene=At3g27340&override=&threshold=18.13&modeMask_low=None&modeMask_stddev=None&gene_alias1=GlcAT14C&gene_alias2=.
DOI: 10.6084/m9.figshare.7082126.v1
title: Additional file 7: of Nogo-B receptor increases the resistance to tamoxifen in estrogen receptor-positive breast cancer cells

description: NgBR (NUS1) mRNA expression data were retrieved from a gene-expression profiling dataset (225071_x from Kaplan–Meier Plot database) of 755 patients with ERα-positive breast cancer and 335 patients with ERα-positive breast cancer treated with endocrine therapy. Kaplan–Meier analysis revealed that the RFS in patients with ERα-positive breast cancer treated with endocrine therapy is significantly decreased in 167 patients with high NgBR expression in tumors as compared to 168 patients with low NgBR expression in tumors (p &lt; 0.05). (XLSX 32 kb)
DOI: 10.6084/m9.figshare.7082168.v1
title: Additional file 9: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S6. Differentially enriched GMMs: The relative abundance and statistical test of the GMMs. (XLS 394 kb)
DOI: 10.6084/m9.figshare.7081931.v1
title: Additional file 3: of Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration

description: Fertility segregations of the BC4 and BC5 populations. A chi-squared test was used to evaluate the fertility segregation ratios. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7082027.v1
title: Additional file 5: of Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa

description: Table S4. Pathogen-infected rice microarray and RNA-Seq data used in this study. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7082036
title: Additional file 11: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S7. The VFG: The relative abundance and statistical test of the VFGs. (XLS 3741 kb)
DOI: 10.6084/m9.figshare.7082162
title: Additional file 9: of Nogo-B receptor increases the resistance to tamoxifen in estrogen receptor-positive breast cancer cells

description: Survivin (BIRC5) mRNA expression data were retrieved from a gene-expression profiling dataset (202094_x from Kaplan–Meier Plot database) of 2046 patients with ERα-positive breast cancer and 928 patients with ERα-positive breast cancer treated with endocrine therapy. Kaplan–Meier analysis revealed that RFS in patients with ERα-positive breast cancer treated with endocrine therapy is significantly decreased in 463 patients with high survivin expression in tumors as compared to 465 patients with low NgBR expression in tumors (p &lt; 0.05). (XLSX 60 kb)
DOI: 10.6084/m9.figshare.24117213.v1
title: Effective <i>Agrobacterium</i>-mediated genetic transformation of okra (<i>Abelmoschus esculentus</i> L.) and generation of RNAi plants resistant to <i>Begomovirus</i> infecting okra

description: Okra is an important vegetable crop of the Malvaceae family and is infected by varying numbers of viruses of the genus <i>Begomovirus</i>. Regardless of the importance of the crop, very little consideration has been given to its genetic improvement. RNA interference (RNAi), a potent biotechnological tool, is known to control <i>Begomovirus</i> in many crops. For the implementation of successful RNAi, there is a need for an efficient genetic transformation system in okra. In the present study, we developed a procedure for <i>Agrobacterium</i>-mediated tissue culture–dependent regeneration of okra plants for the application of RNAi. Eleven transgenic okra RNAi plants were regenerated by utilising hypocotyls as explants. Transformed plants were screened with hygromycin at the regeneration stage and the presence of transgenes (<i>AC1</i>, <i>AC2</i> & <i>AC4</i> codes for replication-associated protein, transcriptional activator protein and suppressor of PTGS) in putative transformed plants was confirmed by polymerase chain reaction (PCR). Wild and transgenic lines were challenged with a dimeric <i>Begomovirus</i> clone or viruliferous whiteflies and the level of resistance was estimated with quantitative real-time reverse transcriptase PCR (qRT-PCR) by utilising viral gene–specific primers. The resistant transgenic lines accumulated very low titres of viral gene products according to the qRT-PCR assays compared to the control plants. This is the first report of tissue culture–mediated RNAi-derived resistance in okra against <i>Begomovirus</i> infection.
DOI: 10.6084/m9.figshare.7082162.v1
title: Additional file 9: of Nogo-B receptor increases the resistance to tamoxifen in estrogen receptor-positive breast cancer cells

description: Survivin (BIRC5) mRNA expression data were retrieved from a gene-expression profiling dataset (202094_x from Kaplan–Meier Plot database) of 2046 patients with ERα-positive breast cancer and 928 patients with ERα-positive breast cancer treated with endocrine therapy. Kaplan–Meier analysis revealed that RFS in patients with ERα-positive breast cancer treated with endocrine therapy is significantly decreased in 463 patients with high survivin expression in tumors as compared to 465 patients with low NgBR expression in tumors (p &lt; 0.05). (XLSX 60 kb)
DOI: 10.6084/m9.figshare.9179138
title: ALS-FTLD-linked mutations of SQSTM1/p62 disrupt selective autophagy and NFE2L2/NRF2 anti-oxidative stress pathway

description: Macroautophagy (autophagy) is a key catabolic pathway for the maintenance of proteostasis through constant digestion of selective cargoes. The selectivity of autophagy is mediated by autophagy receptors that recognize and recruit cargoes to autophagosomes. SQSTM1/p62 is a prototype autophagy receptor, which is commonly found in protein aggregates associated with major neurodegenerative diseases. While accumulation of SQSTM1 implicates a disturbance of selective autophagy pathway, the pathogenic mechanism that contributes to impaired autophagy degradation remains poorly characterized. Herein we show that amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD)-linked mutations of <i>TBK1</i> and <i>SQSTM1</i> disrupt selective autophagy and cause neurotoxicity. Our data demonstrates that proteotoxic stress activates serine/threonine kinase TBK1, which coordinates with autophagy kinase ULK1 to promote concerted phosphorylation of autophagy receptor SQSTM1 at the UBA domain and activation of selective autophagy. In contrast, ALS-FTLD-linked mutations of <i>TBK1</i> or <i>SQSTM1</i> reduce SQSTM1 phosphorylation and compromise ubiquitinated cargo binding and clearance. Moreover, disease mutation SQSTM1<sup>G427R</sup> abolishes phosphorylation of Ser351 and impairs KEAP1-SQSTM1 interaction, thus diminishing NFE2L2/Nrf2-targeted gene expression and increasing TARDBP/TDP-43 associated stress granule formation under oxidative stress. Furthermore, expression of SQSTM1<sup>G427R</sup> in neurons impairs dendrite morphology and KEAP1-NFE2L2 signaling. Therefore, our results reveal a mechanism whereby pathogenic SQSTM1 mutants inhibit selective autophagy and disrupt NFE2L2 anti-oxidative stress response underlying the neurotoxicity in ALS-FTLD. <b>Abbreviations:</b> ALS: amyotrophic lateral sclerosis; FTLD: frontotemporal lobar degeneration; G3BP1: GTPase-activating protein (SH3 domain) binding protein 1; GSTM1: glutathione S-transferase, mu 1; HMOX/HO-1: Heme oxygenase 1; IP: immunoprecipitation; KEAP1: kelch-like ECH associated protein 1; KI: kinase inactive; KIR: KEAP1 interaction region; KO: knockout; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MBP: maltose binding protein; NBR1: NBR1, autophagy cargo receptor; NFE2L2/Nrf2: nuclear factor, erythroid derived 2, like 2; NQO1: NAD(P)H quinone dehydrogenase 1; SQSTM1/p62: sequestosome 1; SOD1: superoxide dismutase 1, soluble; S.S.: serum starvation; TARDBP/TDP-43: TAR DNA binding protein; TBK1: TANK binding kinase 1; UBA: <i>ub</i>iquitin <i>a</i>ssociation; ULK1: unc-51 like autophagy activating kinase 1; WT: wild type.
DOI: 10.6084/m9.figshare.19663872.v1
title: Additional file 2 of Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

description: Additional file 2: Table S1: Overview of the top 19 EnTDefs, including the ranks, enhancer/enhancer-gene link methods, and basic summary statistics. Table S2: The 31 ENCODE ChIP-seq datasets from 9 completely different cell lines and 14 completely different transcription factors. Table S3: The nine ChIA-PET datasets used for generating cell-type-specific EnTDefs (CT-EnTDefs) and number of TFs assayed by ENCODE ChIP-seq in each particular cell type, which were used to evaluate the performance of the CT-EnTDefs. Table S4: Overview of the seven independent datasets used for the comparative analysis. Table S5: ChIA-PET datasets used by “ChIA” and “Loop” methods to assign enhancer to target genes in a cell-type independent manner (general EnTDefs). Table S6: The 87 ENCODE ChIP-seq datasets used for EnTDef evaluation (evaluation ChIP-seq) (tab 1) and the TF vs. cell type matrix (tab 2). Table S7: The 13 ENCODE ChIP-seq datasets from 4 different cell lines (testing ChIP-seq).
DOI: 10.6084/m9.figshare.19663872
title: Additional file 2 of Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

description: Additional file 2: Table S1: Overview of the top 19 EnTDefs, including the ranks, enhancer/enhancer-gene link methods, and basic summary statistics. Table S2: The 31 ENCODE ChIP-seq datasets from 9 completely different cell lines and 14 completely different transcription factors. Table S3: The nine ChIA-PET datasets used for generating cell-type-specific EnTDefs (CT-EnTDefs) and number of TFs assayed by ENCODE ChIP-seq in each particular cell type, which were used to evaluate the performance of the CT-EnTDefs. Table S4: Overview of the seven independent datasets used for the comparative analysis. Table S5: ChIA-PET datasets used by “ChIA” and “Loop” methods to assign enhancer to target genes in a cell-type independent manner (general EnTDefs). Table S6: The 87 ENCODE ChIP-seq datasets used for EnTDef evaluation (evaluation ChIP-seq) (tab 1) and the TF vs. cell type matrix (tab 2). Table S7: The 13 ENCODE ChIP-seq datasets from 4 different cell lines (testing ChIP-seq).
DOI: 10.6084/m9.figshare.12324845
title: Additional file 2 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S1. Summary and statistics of icSHAPE, RNA-seq and iCLIP.
DOI: 10.6084/m9.figshare.24117214
title: Effect of microclimate and photosynthesis on strawberry reproductive growth in a greenhouse: using cumulative leaf photosynthesis as an index to predict the time of harvest

description: We evaluate whether cumulative photosynthesis (<i>A</i><sub>n,C</sub>) could predict the time of harvest in strawberry better than light (<i>I</i><sub>C</sub>) or temperature (<i>T</i><sub>a,C</sub>) as forecast indices. We monitored the daily dynamics of flowering, fruit set, and harvest in over 2,700 fruits across the growing season in a greenhouse in Japan. Photosynthesis was calculated using a biochemical model, and <i>A</i><sub>n,C</sub> calculated by totalling the cumulative rate from flowering to harvest in each fruit. <i>I</i><sub>C</sub> and <i>T</i><sub>a,C</sub> were calculated by totalling daily cumulative light intensity and average temperature. A new index (<i>D</i>) was defined as the normalised variation of <i>A</i><sub>n,C</sub>, <i>I</i><sub>C</sub>, and <i>T</i><sub>a,C</sub>, and a statistical analysis was conducted on the means for each index. The results showed that <i>A</i><sub>n,C</sub> had the lowest <i>D</i> (0.114), suggesting that it was a better index for predicting the time of harvest. This study suggests the importance of considering the accumulation of photosynthates in individual fruit, which cannot be achieved by <i>I</i><sub>C</sub> or <i>T</i><sub>a,C</sub>, these results can be used to improve the forecasting and optimisation of yield. However, further research is required to substantiate these claims.
DOI: 10.6084/m9.figshare.7082051
title: Additional file 1: of A metagenome-wide association study of gut microbiota in asthma in UK adults

description: Table S1. Sample information: The clinical and sequencing information of the sample. (XLS 71 kb)
DOI: 10.6084/m9.figshare.9179138.v1
title: ALS-FTLD-linked mutations of SQSTM1/p62 disrupt selective autophagy and NFE2L2/NRF2 anti-oxidative stress pathway

description: Macroautophagy (autophagy) is a key catabolic pathway for the maintenance of proteostasis through constant digestion of selective cargoes. The selectivity of autophagy is mediated by autophagy receptors that recognize and recruit cargoes to autophagosomes. SQSTM1/p62 is a prototype autophagy receptor, which is commonly found in protein aggregates associated with major neurodegenerative diseases. While accumulation of SQSTM1 implicates a disturbance of selective autophagy pathway, the pathogenic mechanism that contributes to impaired autophagy degradation remains poorly characterized. Herein we show that amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD)-linked mutations of <i>TBK1</i> and <i>SQSTM1</i> disrupt selective autophagy and cause neurotoxicity. Our data demonstrates that proteotoxic stress activates serine/threonine kinase TBK1, which coordinates with autophagy kinase ULK1 to promote concerted phosphorylation of autophagy receptor SQSTM1 at the UBA domain and activation of selective autophagy. In contrast, ALS-FTLD-linked mutations of <i>TBK1</i> or <i>SQSTM1</i> reduce SQSTM1 phosphorylation and compromise ubiquitinated cargo binding and clearance. Moreover, disease mutation SQSTM1<sup>G427R</sup> abolishes phosphorylation of Ser351 and impairs KEAP1-SQSTM1 interaction, thus diminishing NFE2L2/Nrf2-targeted gene expression and increasing TARDBP/TDP-43 associated stress granule formation under oxidative stress. Furthermore, expression of SQSTM1<sup>G427R</sup> in neurons impairs dendrite morphology and KEAP1-NFE2L2 signaling. Therefore, our results reveal a mechanism whereby pathogenic SQSTM1 mutants inhibit selective autophagy and disrupt NFE2L2 anti-oxidative stress response underlying the neurotoxicity in ALS-FTLD. <b>Abbreviations:</b> ALS: amyotrophic lateral sclerosis; FTLD: frontotemporal lobar degeneration; G3BP1: GTPase-activating protein (SH3 domain) binding protein 1; GSTM1: glutathione S-transferase, mu 1; HMOX/HO-1: Heme oxygenase 1; IP: immunoprecipitation; KEAP1: kelch-like ECH associated protein 1; KI: kinase inactive; KIR: KEAP1 interaction region; KO: knockout; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MBP: maltose binding protein; NBR1: NBR1, autophagy cargo receptor; NFE2L2/Nrf2: nuclear factor, erythroid derived 2, like 2; NQO1: NAD(P)H quinone dehydrogenase 1; SQSTM1/p62: sequestosome 1; SOD1: superoxide dismutase 1, soluble; S.S.: serum starvation; TARDBP/TDP-43: TAR DNA binding protein; TBK1: TANK binding kinase 1; UBA: <i>ub</i>iquitin <i>a</i>ssociation; ULK1: unc-51 like autophagy activating kinase 1; WT: wild type.
DOI: 10.6084/m9.figshare.12324848.v1
title: Additional file 3 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S2. LFQ intensity of proteins in UV+ and UV- samples at 0, 0.4 and 4 h.p.f.
DOI: 10.6084/m9.figshare.12324860
title: Additional file 7 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S6. Elavl1a binding sites at 4 h.p.f. Elavl1a binding sites identified by Flag-Elavl1a iCLIP at 4 h.p.f. and 6 h.p.f.
DOI: 10.6084/m9.figshare.12324860.v1
title: Additional file 7 of RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function

description: Table S6. Elavl1a binding sites at 4 h.p.f. Elavl1a binding sites identified by Flag-Elavl1a iCLIP at 4 h.p.f. and 6 h.p.f.