cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6858929.v1
title: Additional file 7: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: RNA-Seq validation using real-time Q-PCR. a. Comparison of expression values obtained from Q-PCR and RNA-Seq normalized to WT control (normal). The analysis was performed on two different reference genes separately (CYCP2 (AT3G21870) and UBQ7 (AT2G35635)). b. Primer sequences used for real-time Q-PCR. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6858902
title: Additional file 5: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: A transcript profile comparison to evaluate purity of pollen samples used for RNA-Seq. A subset of 12 genes was used to compare relative purities of pollen samples in the current pollen transcriptome study to those from a RNA-Seq study from Loraine et al. [22] (yellow highlights) or a microarray experiment from Qin et al. 2009 [23] (purple highlights). Four references genes were chosen to generate normalization factors that could be used to adjust expression values in Loraine et al. [22] and Qin et al. 2009 [23] to allow a relative comparison of the three data sets for WT pollen under control (normal) conditions. For a control group, three CNGC genes were chosen that displayed low to moderate levels of expression (Tunc-Ozdemir et al. 2013 [24] and Frietsch et al. 2007 [25]). As markers for potential contamination from photosynthetic tissues, five different nuclear encoded genes were chosen that are associated with either photosystems I/II, or chlorophyll A-B binding proteins (Umate 2010 [26]). Average relative ratios are shown for each of the four different pollen samples in comparison to both Loraine et al. [22] and Qin et al. [23]. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6858902.v1
title: Additional file 5: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: A transcript profile comparison to evaluate purity of pollen samples used for RNA-Seq. A subset of 12 genes was used to compare relative purities of pollen samples in the current pollen transcriptome study to those from a RNA-Seq study from Loraine et al. [22] (yellow highlights) or a microarray experiment from Qin et al. 2009 [23] (purple highlights). Four references genes were chosen to generate normalization factors that could be used to adjust expression values in Loraine et al. [22] and Qin et al. 2009 [23] to allow a relative comparison of the three data sets for WT pollen under control (normal) conditions. For a control group, three CNGC genes were chosen that displayed low to moderate levels of expression (Tunc-Ozdemir et al. 2013 [24] and Frietsch et al. 2007 [25]). As markers for potential contamination from photosynthetic tissues, five different nuclear encoded genes were chosen that are associated with either photosystems I/II, or chlorophyll A-B binding proteins (Umate 2010 [26]). Average relative ratios are shown for each of the four different pollen samples in comparison to both Loraine et al. [22] and Qin et al. [23]. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6858875
title: Additional file 3: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: Normalized transcript expression counts for WT and cngc16 pollen with and without HS. Expression counts from Additional file 2 were subjected to exclusions/filters and normalized as described in methods. Expression data from other transcriptome studies (microarray and RNA-Seq) were added to the table for comparisons. These included an RNA-Seq data set for WT pollen and seedlings from Loraine et al. 2013 (PMCID: PMC3668042 [22]), two pollen microarray experiments from Qin et al. 2009 (PMCID: PMC2726614 [23]) and Borges et al. 2008 (PMCID: PMC2556834 [72]), and finally HS seedlings from Schmid et al. 2005 (PMID:15806101 [33]), respectively. Ratios of expression between pollen and seedling are based on Loraine et al. 2013 (PMCID: PMC3668042 [22]). In cases where the seedling value was below the limit of detection, a minimal value of 0.0019 was substituted in its place as a denominator (0.0019 was the RPKM for ATCG00860 and was the lowest value reported in Loraine et al. 2013 (PMCID: PMC3668042 [22]). Ratio of expression between semi-in vivo pollen tube over dry pollen is based on Qin et al. 2009 (PMCID: PMC2726614 [23]). HS dependent changes in transcript abundance in shoots were based on publicly available data using the AtGenExpress Visualization Tool (AVT) ( http://jsp.weigelworld.org/expviz/expviz.jsp , Schmid et al. 2005 (PMID:15806101 [33] for seedlings exposed to one hour HS at 38Â Â°C). The log2-fold change was calculated based on a comparison of means of normalized values for two heat-stressed and two non-stressed seedling samples. NA stands for not available. Not Calculated, refers to a value not being calculated because one of the input sample read counts was considered to have an extreme outlier (see AT2G42540 and ATMG01360). (XLSX 8952 kb)
DOI: 10.6084/m9.figshare.6858875.v1
title: Additional file 3: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: Normalized transcript expression counts for WT and cngc16 pollen with and without HS. Expression counts from Additional file 2 were subjected to exclusions/filters and normalized as described in methods. Expression data from other transcriptome studies (microarray and RNA-Seq) were added to the table for comparisons. These included an RNA-Seq data set for WT pollen and seedlings from Loraine et al. 2013 (PMCID: PMC3668042 [22]), two pollen microarray experiments from Qin et al. 2009 (PMCID: PMC2726614 [23]) and Borges et al. 2008 (PMCID: PMC2556834 [72]), and finally HS seedlings from Schmid et al. 2005 (PMID:15806101 [33]), respectively. Ratios of expression between pollen and seedling are based on Loraine et al. 2013 (PMCID: PMC3668042 [22]). In cases where the seedling value was below the limit of detection, a minimal value of 0.0019 was substituted in its place as a denominator (0.0019 was the RPKM for ATCG00860 and was the lowest value reported in Loraine et al. 2013 (PMCID: PMC3668042 [22]). Ratio of expression between semi-in vivo pollen tube over dry pollen is based on Qin et al. 2009 (PMCID: PMC2726614 [23]). HS dependent changes in transcript abundance in shoots were based on publicly available data using the AtGenExpress Visualization Tool (AVT) ( http://jsp.weigelworld.org/expviz/expviz.jsp , Schmid et al. 2005 (PMID:15806101 [33] for seedlings exposed to one hour HS at 38Â Â°C). The log2-fold change was calculated based on a comparison of means of normalized values for two heat-stressed and two non-stressed seedling samples. NA stands for not available. Not Calculated, refers to a value not being calculated because one of the input sample read counts was considered to have an extreme outlier (see AT2G42540 and ATMG01360). (XLSX 8952 kb)
DOI: 10.6084/m9.figshare.6858860
title: Additional file 2: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: Raw expression counts for WT and cngc16 pollen with and without HS. Read counts generated via FeatureCounts, see Methods) for all 12 replicates are shown before normalization and exclusions. (XLSX 4358 kb)
DOI: 10.6084/m9.figshare.6858860.v1
title: Additional file 2: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: Raw expression counts for WT and cngc16 pollen with and without HS. Read counts generated via FeatureCounts, see Methods) for all 12 replicates are shown before normalization and exclusions. (XLSX 4358 kb)
DOI: 10.6084/m9.figshare.6858830
title: Additional file 5: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

description: Supplementary data (A and B). Results of simulation quality assessment. (ZIP 8405 kb)
DOI: 10.6084/m9.figshare.6858830.v1
title: Additional file 5: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

description: Supplementary data (A and B). Results of simulation quality assessment. (ZIP 8405 kb)
DOI: 10.6084/m9.figshare.6858821
title: Additional file 4: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

description: Supplementary data. Detailed results from the study of DE toolsâ recovering ability of biological truth. (HTML 2102 kb)
DOI: 10.6084/m9.figshare.6858821.v1
title: Additional file 4: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

description: Supplementary data. Detailed results from the study of DE toolsâ recovering ability of biological truth. (HTML 2102 kb)
DOI: 10.6084/m9.figshare.6858797
title: Additional file 3: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

description: Supplementary data. Detailed results of concordance analysis of DE tools. (HTML 15901 kb)
DOI: 10.6084/m9.figshare.6858797.v1
title: Additional file 3: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

description: Supplementary data. Detailed results of concordance analysis of DE tools. (HTML 15901 kb)
DOI: 10.6084/m9.figshare.6858794
title: Additional file 13: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: A comparison of HS-dependent changes in pollen to 67 multi-stress response genes in vegetative tissues. From a list of 67 multi-stress genes curated by Swindell 2006 (PMCID: PMC1698639 [47]; highlighted in purple), 19 genes showed detectable expression in pollen. Among those, only three genes showed significant changes in pollen HS (red font). (XLSX 596 kb)
DOI: 10.6084/m9.figshare.6858794.v1
title: Additional file 13: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: A comparison of HS-dependent changes in pollen to 67 multi-stress response genes in vegetative tissues. From a list of 67 multi-stress genes curated by Swindell 2006 (PMCID: PMC1698639 [47]; highlighted in purple), 19 genes showed detectable expression in pollen. Among those, only three genes showed significant changes in pollen HS (red font). (XLSX 596 kb)
DOI: 10.6084/m9.figshare.6858782
title: Additional file 2: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

description: Supplementary data. Detailed results of comparisons of normalization methods. (HTML 2067 kb)
DOI: 10.6084/m9.figshare.6858782.v1
title: Additional file 2: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

description: Supplementary data. Detailed results of comparisons of normalization methods. (HTML 2067 kb)
DOI: 10.6084/m9.figshare.6858773
title: Additional file 12: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: 230 Genes with putative Ca2+-signaling related functions. 230 genes with putative Ca2+-signaling related functions were identified here with quantifiable expression levels in the pollen RNA-Seq data set. Of those 230, 40 genes (yellow highlights) showed HS-dependent changes (≥ 2-fold changes with adjusted p-value ≤0.01) in WT pollen. Similar HS-dependent changes were also observed for cngc16 mutant, with seven potential exceptions with lower degrees of significance shown in bold. a Ratio of expression between pollen and seedling is based on Loraine et al. 2013 (PMCID: PMC3668042 [22]). b A comparison is provided to HS-dependent changes observed for aerial parts of seedlings exposed to a one hour 38 °C HS based on publicly available microarray data in AtGenExpress, ( http://jsp.weigelworld.org/expviz/expviz.jsp ; Schmid et al. 2005 (PMID: 15806101 [33]). The log2-fold change was calculated based on means of normalized values for two heat-stressed seedlings compared to two non-stressed seedlings. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6858770
title: Additional file 4 of Accounting for location uncertainty in azimuthal telemetry data improves ecological inference

description: R code to simulate azimuthal data under different study designs and fit the azimuthal telemetry model. (ZIP 50 kb)
DOI: 10.6084/m9.figshare.6858773.v1
title: Additional file 12: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: 230 Genes with putative Ca2+-signaling related functions. 230 genes with putative Ca2+-signaling related functions were identified here with quantifiable expression levels in the pollen RNA-Seq data set. Of those 230, 40 genes (yellow highlights) showed HS-dependent changes (≥ 2-fold changes with adjusted p-value ≤0.01) in WT pollen. Similar HS-dependent changes were also observed for cngc16 mutant, with seven potential exceptions with lower degrees of significance shown in bold. a Ratio of expression between pollen and seedling is based on Loraine et al. 2013 (PMCID: PMC3668042 [22]). b A comparison is provided to HS-dependent changes observed for aerial parts of seedlings exposed to a one hour 38 °C HS based on publicly available microarray data in AtGenExpress, ( http://jsp.weigelworld.org/expviz/expviz.jsp ; Schmid et al. 2005 (PMID: 15806101 [33]). The log2-fold change was calculated based on means of normalized values for two heat-stressed seedlings compared to two non-stressed seedlings. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6858770.v1
title: Additional file 4 of Accounting for location uncertainty in azimuthal telemetry data improves ecological inference

description: R code to simulate azimuthal data under different study designs and fit the azimuthal telemetry model. (ZIP 50 kb)
DOI: 10.6084/m9.figshare.6858755
title: Additional file 11: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: HS-dependent transcript abundance changes corresponding to transcription factors in WT and cngc16 pollen. Differentially expressed transcription factors (TFs) are organized to show HS-dependent differences that are WT-specific (23 changes, yellow highlight), cngc16-specific (98 changes, blue highlight), or common to both mutant and WT (66 changes, white highlight). a A comparison is provided to HS-dependent changes observed for aerial parts of seedlings exposed to a one hour 38Â Â°C HS based on publicly available microarray data in AtGenExpress, ( http://jsp.weigelworld.org/expviz/expviz.jsp ; Schmid et al. 2005 (PMID: 15806101 [34]). The log2-fold change was calculated based on means of normalized values for two heat-stressed seedlings compared to two non-stressed seedlings. NA stands for not available because of absence of probeset on microarray experiment. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.6858755.v1
title: Additional file 11: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: HS-dependent transcript abundance changes corresponding to transcription factors in WT and cngc16 pollen. Differentially expressed transcription factors (TFs) are organized to show HS-dependent differences that are WT-specific (23 changes, yellow highlight), cngc16-specific (98 changes, blue highlight), or common to both mutant and WT (66 changes, white highlight). a A comparison is provided to HS-dependent changes observed for aerial parts of seedlings exposed to a one hour 38Â Â°C HS based on publicly available microarray data in AtGenExpress, ( http://jsp.weigelworld.org/expviz/expviz.jsp ; Schmid et al. 2005 (PMID: 15806101 [34]). The log2-fold change was calculated based on means of normalized values for two heat-stressed seedlings compared to two non-stressed seedlings. NA stands for not available because of absence of probeset on microarray experiment. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.6858737
title: Additional file 10: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: Association network for HS-dependent changes in WT that were most different in cngc16 under HS. The figure was generated using STRING [32] and the top 23 genes identified in Table 3. (XLSX 154 kb)
DOI: 10.6084/m9.figshare.6858737.v1
title: Additional file 10: of A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16)

description: Association network for HS-dependent changes in WT that were most different in cngc16 under HS. The figure was generated using STRING [32] and the top 23 genes identified in Table 3. (XLSX 154 kb)
DOI: 10.6084/m9.figshare.6858713
title: Additional file 1: of Determination of sialic acid in saliva by means of surface-enhanced Raman spectroscopy as a marker in adnexal mass patients: ovarian cancer vs benign cases

description: Patients data participating in the sialic acid determination. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6858713.v1
title: Additional file 1: of Determination of sialic acid in saliva by means of surface-enhanced Raman spectroscopy as a marker in adnexal mass patients: ovarian cancer vs benign cases

description: Patients data participating in the sialic acid determination. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6858686
title: Additional file 2: of Prospective observations study protocol to investigate cost-effectiveness of various prenatal test strategies after the introduction of noninvasive prenatal testing

description: Physicians Questionnaire: Korean version and Physicians Questionnaire: English version. (ZIP 536 kb)
DOI: 10.6084/m9.figshare.6858686.v1
title: Additional file 2: of Prospective observations study protocol to investigate cost-effectiveness of various prenatal test strategies after the introduction of noninvasive prenatal testing

description: Physicians Questionnaire: Korean version and Physicians Questionnaire: English version. (ZIP 536 kb)
DOI: 10.6084/m9.figshare.6858668
title: Additional file 1: of Prospective observations study protocol to investigate cost-effectiveness of various prenatal test strategies after the introduction of noninvasive prenatal testing

description: Patients Questionnaire: Korean version and Patients Quesionnaire:Â English version. (ZIP 524 kb)
DOI: 10.6084/m9.figshare.6858662
title: Additional file 1: of Cenani-Lenz syndactyly syndrome - a case report of a family with isolated syndactyly

description: Table S1. Variant data â Data related to Whole Exome Sequencing (WES). (XLSX 274 kb)
DOI: 10.6084/m9.figshare.6858668.v1
title: Additional file 1: of Prospective observations study protocol to investigate cost-effectiveness of various prenatal test strategies after the introduction of noninvasive prenatal testing

description: Patients Questionnaire: Korean version and Patients Quesionnaire:Â English version. (ZIP 524 kb)
DOI: 10.6084/m9.figshare.6858662.v1
title: Additional file 1: of Cenani-Lenz syndactyly syndrome - a case report of a family with isolated syndactyly

description: Table S1. Variant data â Data related to Whole Exome Sequencing (WES). (XLSX 274 kb)
DOI: 10.6084/m9.figshare.6858566
title: Additional file 5: of Human alveolar epithelial cells type II are capable of TGFÎ˛-dependent epithelial-mesenchymal-transition and collagen-synthesis

description: Table S3. Enriched GO terms. Spreadsheet containing results from network analysis using Cytoscape and the Reactome FIViz app for discovery of interaction modules. Significant enriched GO terms for Biological Process for each module are presented. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.6858566.v1
title: Additional file 5: of Human alveolar epithelial cells type II are capable of TGFÎ˛-dependent epithelial-mesenchymal-transition and collagen-synthesis

description: Table S3. Enriched GO terms. Spreadsheet containing results from network analysis using Cytoscape and the Reactome FIViz app for discovery of interaction modules. Significant enriched GO terms for Biological Process for each module are presented. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.6858551
title: Additional file 4: of Human alveolar epithelial cells type II are capable of TGFÎ˛-dependent epithelial-mesenchymal-transition and collagen-synthesis

description: Table S2. Results from Reactome FIViz module analysis. Spreadsheet containing results from network analysis using Cytoscape and the Reactome FIViz app for discovery of interaction modules. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6858551.v1
title: Additional file 4: of Human alveolar epithelial cells type II are capable of TGFÎ˛-dependent epithelial-mesenchymal-transition and collagen-synthesis

description: Table S2. Results from Reactome FIViz module analysis. Spreadsheet containing results from network analysis using Cytoscape and the Reactome FIViz app for discovery of interaction modules. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6858545
title: Additional file 3: of Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project

description: Table S2.The imputation coverage (proportion of variants with confidence: imputation r2 â Ľ0.8) across different non-reference allele frequency bins and the number of variants that were efficiently imputed.Â (CSV 20 kb)
DOI: 10.6084/m9.figshare.6858545.v1
title: Additional file 3: of Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project

description: Table S2.The imputation coverage (proportion of variants with confidence: imputation r2 â Ľ0.8) across different non-reference allele frequency bins and the number of variants that were efficiently imputed.Â (CSV 20 kb)
DOI: 10.6084/m9.figshare.6858536
title: Additional file 3: of Human alveolar epithelial cells type II are capable of TGFÎ˛-dependent epithelial-mesenchymal-transition and collagen-synthesis

description: Table S1. Results from 1Â W-ANOVA for regulation between experimental groups. Spreadsheet containing microarray data from statistical analysis. (XLSX 2864 kb)
DOI: 10.6084/m9.figshare.6858536.v1
title: Additional file 3: of Human alveolar epithelial cells type II are capable of TGFÎ˛-dependent epithelial-mesenchymal-transition and collagen-synthesis

description: Table S1. Results from 1Â W-ANOVA for regulation between experimental groups. Spreadsheet containing microarray data from statistical analysis. (XLSX 2864 kb)