cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8332406
title: Supplementary Material for: A Search for Sex-Linked Loci in the Agamid Lizard, Calotes versicolor

description: The Indian garden lizard, <i>Calotes versicolor</i>, lacks cytologically recognizable sex chromosomes, and its mechanism of sex determination is unclear. We evaluated genotype-to-sex-phenotype association using RAD-seq in wild-caught males and females, 30 of each sex. Of 210,736 unique, 96-nt long RAD-tags, 48% contained polymorphisms, 23% of which were present in at least 40 of 60 individuals. Twenty one RAD-tags neared, but none achieved, the inclusion criteria for sex enrichment, as expected if <i>C. versicolor</i> lacks highly differentiated sex chromosomes. Three RAD-tags with alleles most strongly associated with sex tended to be heterozygous in females and to lack male-specific alleles, suggesting a ZW female/ZZ male system. Putative female alleles, however, were present in some males and lacking from some females, suggesting either recombination between these markers and the sex locus or sex reversal due to environmental or genetic factors. Paired-end, 250-nt reads from 1 male provided a fragmented draft genome assembly. Four sex-associated RAD-tags were identical to portions of 4 unique <i>C. versicolor </i>genomic contigs rather than linked to a single putative sex-linked region. The lack of strongly sex-linked loci coupled with weak evidence for temperature-associated sex determination intensifies the need for further investigation of the puzzling sex determination mechanism in <i>C. versicolor</i>.
DOI: 10.6084/m9.figshare.8332406.v1
title: Supplementary Material for: A Search for Sex-Linked Loci in the Agamid Lizard, Calotes versicolor

description: The Indian garden lizard, <i>Calotes versicolor</i>, lacks cytologically recognizable sex chromosomes, and its mechanism of sex determination is unclear. We evaluated genotype-to-sex-phenotype association using RAD-seq in wild-caught males and females, 30 of each sex. Of 210,736 unique, 96-nt long RAD-tags, 48% contained polymorphisms, 23% of which were present in at least 40 of 60 individuals. Twenty one RAD-tags neared, but none achieved, the inclusion criteria for sex enrichment, as expected if <i>C. versicolor</i> lacks highly differentiated sex chromosomes. Three RAD-tags with alleles most strongly associated with sex tended to be heterozygous in females and to lack male-specific alleles, suggesting a ZW female/ZZ male system. Putative female alleles, however, were present in some males and lacking from some females, suggesting either recombination between these markers and the sex locus or sex reversal due to environmental or genetic factors. Paired-end, 250-nt reads from 1 male provided a fragmented draft genome assembly. Four sex-associated RAD-tags were identical to portions of 4 unique <i>C. versicolor </i>genomic contigs rather than linked to a single putative sex-linked region. The lack of strongly sex-linked loci coupled with weak evidence for temperature-associated sex determination intensifies the need for further investigation of the puzzling sex determination mechanism in <i>C. versicolor</i>.
DOI: 10.6084/m9.figshare.8332385
title: Fermentation screen data all isolates

description: Mass measurements obtained from fermentations using wild yeast isolates within micro-fermenters.
DOI: 10.6084/m9.figshare.8332481.v9
title: Serum osteocalcin predicts HTO-ROD in KTRs

description: <b>Serum osteocalcin predicts HTO-ROD in KTRs</b>
DOI: 10.6084/m9.figshare.8332481.v8
title: Renal osteodystrophy and biomarkers in KTX

description: <b>Serum osteocalcin predicts HTO-ROD in KTRs</b>
DOI: 10.6084/m9.figshare.8332286
title: Study on utilization of Penaeus vannamei for snack food production

description: Standardization of the process of freeze drying of <i>Penaeus vannamei</i> and subsequent development of ready-to-eat freeze dried shrimp snack was conceptualized. Freeze drying of shrimp was standardized to obtain the final moisture content of 3%. The freeze dried shrimp was air fried and oil fried. Five flavours were tried on the product and among these peri peri was selected based on organoleptic evaluation. The storage studies were conducted on freeze dried shrimp snack in comparison with hot air dried shrimp snack packed under air and nitrogen atmosphere for 120 days. Biochemical and microbial analysis were carried out during storage period. The result of analysis showed that the product was good and shelf stable for a period of 120 days.<br>
DOI: 10.6084/m9.figshare.8332274
title: Supplementary Data from Mechanistic dose–response modelling of animal challenge data shows that intact skin is a crucial barrier to leptospiral infection

description: Results from all animal infection experiments (note: document contains multiple tabs).
DOI: 10.6084/m9.figshare.8332286.v1
title: Study on utilization of Penaeus vannamei for snack food production

description: Standardization of the process of freeze drying of <i>Penaeus vannamei</i> and subsequent development of ready-to-eat freeze dried shrimp snack was conceptualized. Freeze drying of shrimp was standardized to obtain the final moisture content of 3%. The freeze dried shrimp was air fried and oil fried. Five flavours were tried on the product and among these peri peri was selected based on organoleptic evaluation. The storage studies were conducted on freeze dried shrimp snack in comparison with hot air dried shrimp snack packed under air and nitrogen atmosphere for 120 days. Biochemical and microbial analysis were carried out during storage period. The result of analysis showed that the product was good and shelf stable for a period of 120 days.<br>
DOI: 10.6084/m9.figshare.8332274.v1
title: Supplementary Data from Mechanistic dose–response modelling of animal challenge data shows that intact skin is a crucial barrier to leptospiral infection

description: Results from all animal infection experiments (note: document contains multiple tabs).
DOI: 10.6084/m9.figshare.8331776
title: compare functional significance of race, age, gender and career category

description: compare functional significance of race, age, gender and career category
DOI: 10.6084/m9.figshare.8331779
title: Aiptasia_pallida_heatStress_peaks

description: This analysis is the product of ATAC-seq experiment done in Aiptasia pallida. <br>These files are peaks BED files dirived from MACS2.<br><br>
DOI: 10.6084/m9.figshare.8331776.v1
title: compare functional significance of race, age, gender and career category

description: compare functional significance of race, age, gender and career category
DOI: 10.6084/m9.figshare.8331425
title: Additional file 7: of Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy

description: Table S5. Parental read counts per each analyzed SNP in the placental RNA-Seq dataset across the full study sample and in the clinical subgroups. (XLSX 141 kb)
DOI: 10.6084/m9.figshare.8331428
title: Additional file 8: of Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy

description: Table S6. Binominal test results assessing the parental allelic proportions in the placental RNA-Seq dataset and background information on the placental expression level and overall expressional breadth of the analyzed genes across tissues. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8331428.v1
title: Additional file 8: of Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy

description: Table S6. Binominal test results assessing the parental allelic proportions in the placental RNA-Seq dataset and background information on the placental expression level and overall expressional breadth of the analyzed genes across tissues. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8331425.v1
title: Additional file 7: of Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy

description: Table S5. Parental read counts per each analyzed SNP in the placental RNA-Seq dataset across the full study sample and in the clinical subgroups. (XLSX 141 kb)
DOI: 10.6084/m9.figshare.8331416
title: Additional file 4: of Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy

description: Table S3. Filtering pipeline for the imprinting candidate genes to be included in the analysis in the current study. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.8331416.v1
title: Additional file 4: of Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy

description: Table S3. Filtering pipeline for the imprinting candidate genes to be included in the analysis in the current study. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.8331338
title: Additional file 2 of Comparison of a time-varying covariate model and a joint model of time-to-event outcomes in the presence of measurement error and interval censoring: application to kidney transplantation

description: ∙ example-1-JM.R: Code to fit M1 ∙ longitudinal-data.csv: simulated TAC data for M1 ∙ survival-data.csv: simulated dnDSA data for M1 ∙ model-1-JM.txt: JAGS model, called by example-1-JM.R ∙ example-1-NLMIXED.SAS: Code to fit M1 with PROC NLMIXED, uses same simulated data ∙ example-4-TVC.R: Code to fit M4 ∙ longitudinal data tvc.csv: simulated TAC data for M4 (carried forward values of TAC) ∙ model-4-TVC.txt: JAGS model, called by example-4-TVC.R (ZIP 199 kb)
DOI: 10.6084/m9.figshare.8331338.v1
title: Additional file 2 of Comparison of a time-varying covariate model and a joint model of time-to-event outcomes in the presence of measurement error and interval censoring: application to kidney transplantation

description: ∙ example-1-JM.R: Code to fit M1 ∙ longitudinal-data.csv: simulated TAC data for M1 ∙ survival-data.csv: simulated dnDSA data for M1 ∙ model-1-JM.txt: JAGS model, called by example-1-JM.R ∙ example-1-NLMIXED.SAS: Code to fit M1 with PROC NLMIXED, uses same simulated data ∙ example-4-TVC.R: Code to fit M4 ∙ longitudinal data tvc.csv: simulated TAC data for M4 (carried forward values of TAC) ∙ model-4-TVC.txt: JAGS model, called by example-4-TVC.R (ZIP 199 kb)
DOI: 10.6084/m9.figshare.8331248
title: Additional file 9: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Read mapping details. Total number of input reads and read mapping details, based on TopHat2 output reports, are shown for the two varieties. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8331248.v1
title: Additional file 9: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Read mapping details. Total number of input reads and read mapping details, based on TopHat2 output reports, are shown for the two varieties. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8331236
title: Additional file 7: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Selected sample correlation coefficients. Pearson correlation coefficients for samples retained in all analyses are reported. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8331236.v1
title: Additional file 7: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Selected sample correlation coefficients. Pearson correlation coefficients for samples retained in all analyses are reported. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8331224
title: Additional file 5: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Spearman correlation coefficients of all sequenced samples, according to RNA-seq ENCODE standard, 2016 [44]. Spearman correlations were calculated using the “cor” function in R “stats” package. Samples highlighted in colours have been subsequently removed from downstream steps, based on the above Pearson correlations as well as sample clustering after Rlog transformation of data. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8331224.v1
title: Additional file 5: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Spearman correlation coefficients of all sequenced samples, according to RNA-seq ENCODE standard, 2016 [44]. Spearman correlations were calculated using the “cor” function in R “stats” package. Samples highlighted in colours have been subsequently removed from downstream steps, based on the above Pearson correlations as well as sample clustering after Rlog transformation of data. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8331212
title: Additional file 3: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: All sample correlation coefficients. Pearson correlation coefficients for all samples originally sequenced are reported. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8331212.v1
title: Additional file 3: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: All sample correlation coefficients. Pearson correlation coefficients for all samples originally sequenced are reported. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8331200
title: Additional file 27: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Sequences of primer pairs designed and used in qRT-PCR for each target gene. Above, primers used for the validation of RNA-Seq technique; below, primers used for the validation of RNA-Seq results, concerning the jasmonate pathway. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8331194
title: Additional file 26: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Co-expression analysis results: enriched GO terms identified for each cluster. Enriched GOs for the Biological Process domain for genes in clusters were calculated with the hypergeometric test as implemented in the Bioconductor GOstats package, using a p-value cutoff of 0.01. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.8331200.v1
title: Additional file 27: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Sequences of primer pairs designed and used in qRT-PCR for each target gene. Above, primers used for the validation of RNA-Seq technique; below, primers used for the validation of RNA-Seq results, concerning the jasmonate pathway. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8331188
title: Additional file 25: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Co-expression analysis results: annotation details for genes identified in each cluster. ID, name, annotation and description of each gene, together with GO annotation, are reported for each cluster. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.8331194.v1
title: Additional file 26: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Co-expression analysis results: enriched GO terms identified for each cluster. Enriched GOs for the Biological Process domain for genes in clusters were calculated with the hypergeometric test as implemented in the Bioconductor GOstats package, using a p-value cutoff of 0.01. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.8331182
title: Additional file 24: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Details of differentially expressed genes involved in hormone-related pathways, cell wall and secondary metabolism modulated by HSt and FDSt at 3 and 6â days post infestation in Chardonnay and Tocai friulano. The bin numbers and names, the id numbers and the description of the genes, and the Log2 fold changes, as obtained from the DESeq2 output, are reported. (XLSX 176 kb)
DOI: 10.6084/m9.figshare.8331188.v1
title: Additional file 25: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Co-expression analysis results: annotation details for genes identified in each cluster. ID, name, annotation and description of each gene, together with GO annotation, are reported for each cluster. (XLSX 78 kb)
DOI: 10.6084/m9.figshare.8331182.v1
title: Additional file 24: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Details of differentially expressed genes involved in hormone-related pathways, cell wall and secondary metabolism modulated by HSt and FDSt at 3 and 6â days post infestation in Chardonnay and Tocai friulano. The bin numbers and names, the id numbers and the description of the genes, and the Log2 fold changes, as obtained from the DESeq2 output, are reported. (XLSX 176 kb)
DOI: 10.6084/m9.figshare.8331164
title: Additional file 21: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Details of Mapman Wilcoxonâ s rank sum test reporting the p-values of different bins modulated in Tocai friulano and represented in Fig. 10. Data concerning bin number and name, the number of DEGs per bin, and the p-values are reported after HSt and FDSt treatments at 3 and 6 dpi. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.8331158
title: Additional file 20: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Details of Mapman Wilcoxonâ s rank sum test reporting the p-values of different bins modulated in Chardonnay and represented in Fig. 9. Data concerning bin number and name, the number of DEGs per bin, and the p-values are reported after HSt and FDSt treatments at 3 and 6 dpi. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.8331164.v1
title: Additional file 21: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Details of Mapman Wilcoxonâ s rank sum test reporting the p-values of different bins modulated in Tocai friulano and represented in Fig. 10. Data concerning bin number and name, the number of DEGs per bin, and the p-values are reported after HSt and FDSt treatments at 3 and 6 dpi. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.8331158.v1
title: Additional file 20: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorĂŠe phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Details of Mapman Wilcoxonâ s rank sum test reporting the p-values of different bins modulated in Chardonnay and represented in Fig. 9. Data concerning bin number and name, the number of DEGs per bin, and the p-values are reported after HSt and FDSt treatments at 3 and 6 dpi. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.8331128
title: Additional file 16: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Enriched GO terms in Tocai friulano after HSt and FDSt attacks. Results of GO enrichment analysis obtained in the “noSt vs. HSt” and “noSt vs. FDSt” comparisons in Tocai friulano at 3 and 6 days post infestation. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.8331128.v1
title: Additional file 16: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Enriched GO terms in Tocai friulano after HSt and FDSt attacks. Results of GO enrichment analysis obtained in the “noSt vs. HSt” and “noSt vs. FDSt” comparisons in Tocai friulano at 3 and 6 days post infestation. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.8331119
title: Additional file 14: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Differentially-expressed genes in Tocai friulano after HSt and FDSt attacks. RNA-Seq results with DEGs obtained in the “noSt vs. HSt” and “noSt vs. FDSt” comparisons in Tocai friulano at 3 and 6 days post infestation. (XLSX 1353 kb)
DOI: 10.6084/m9.figshare.8331122
title: Additional file 15: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Enriched GO terms in Chardonnay after HSt and FDSt attacks. Results of GO enrichment analysis obtained in the “noSt vs. HSt” and “noSt vs. FDSt” comparisons in Chardonnay at 3 and 6 days post infestation. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.8331113
title: Additional file 13: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Differentially-expressed genes in Chardonnay after HSt and FDSt attacks. RNA-Seq results with DEGs obtained in the “noSt vs. HSt” and “noSt vs. FDSt” comparisons in Chardonnay at 3 and 6 days post infestation. (XLSX 1075 kb)
DOI: 10.6084/m9.figshare.8331113.v1
title: Additional file 13: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Differentially-expressed genes in Chardonnay after HSt and FDSt attacks. RNA-Seq results with DEGs obtained in the “noSt vs. HSt” and “noSt vs. FDSt” comparisons in Chardonnay at 3 and 6 days post infestation. (XLSX 1075 kb)
DOI: 10.6084/m9.figshare.8331122.v1
title: Additional file 15: of Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties

description: Enriched GO terms in Chardonnay after HSt and FDSt attacks. Results of GO enrichment analysis obtained in the “noSt vs. HSt” and “noSt vs. FDSt” comparisons in Chardonnay at 3 and 6 days post infestation. (XLSX 54 kb)