cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14551989
title: Additional file 6 of TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae

description: Additional file 6: Table S3. This contains the results of the comparative analyses of transcriptomes of purified spores with germinating spore cultures after 0, 10, 30, 60, 120, 240 and 360-minutes following transfer into YPD in the appropriately labelled worksheets. All worksheets have of the differential transcriptomic analysis in which the values of logFC (FC = fold-change in transcript levels) along with the corresponding logCPM (counts per million), False Discovery Rate (FDR) and P-values are indicated for each gene.
DOI: 10.6084/m9.figshare.14551992
title: Additional file 7 of TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae

description: Additional file 7: Table S4. Tables 1-7 contain the results of the comparative analyses of transcriptomes of ungerminated spores and spores transferred to ‘YPD + rapamycin’ after 0, 10, 30, 60, 120, 240 and 360 minutes following transfer into YPD in the appropriately labelled worksheets All worksheets have the results of the differential transcriptomic analysis in which the values of logFC (FC = fold-change in transcript levels) along with the corresponding logCPM (counts per million), False Discovery Rate (FDR) and P-values are indicated for each gene.
DOI: 10.6084/m9.figshare.14551998.v1
title: Additional file 8 of TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae

description: Additional file 8: Table S5. This contain the results of the comparative analyses of transcriptomes of ‘Spores transferred to YPD + DMSO’ and ‘spores transferred to YPD + rapamycin’ after 0, 10, 30, 60, 120, 240 and 360-minutes following transfer into YPD in the appropriately labelled worksheets. All worksheets have of the differential transcriptomic analysis in which the values of logFC (FC = fold-change in transcript levels) along with the corresponding logCPM (counts per million), False Discovery Rate (FDR) and P-values are indicated for each gene.
DOI: 10.6084/m9.figshare.14551989.v1
title: Additional file 6 of TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae

description: Additional file 6: Table S3. This contains the results of the comparative analyses of transcriptomes of purified spores with germinating spore cultures after 0, 10, 30, 60, 120, 240 and 360-minutes following transfer into YPD in the appropriately labelled worksheets. All worksheets have of the differential transcriptomic analysis in which the values of logFC (FC = fold-change in transcript levels) along with the corresponding logCPM (counts per million), False Discovery Rate (FDR) and P-values are indicated for each gene.
DOI: 10.6084/m9.figshare.14551998
title: Additional file 8 of TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae

description: Additional file 8: Table S5. This contain the results of the comparative analyses of transcriptomes of ‘Spores transferred to YPD + DMSO’ and ‘spores transferred to YPD + rapamycin’ after 0, 10, 30, 60, 120, 240 and 360-minutes following transfer into YPD in the appropriately labelled worksheets. All worksheets have of the differential transcriptomic analysis in which the values of logFC (FC = fold-change in transcript levels) along with the corresponding logCPM (counts per million), False Discovery Rate (FDR) and P-values are indicated for each gene.
DOI: 10.6084/m9.figshare.14551992.v1
title: Additional file 7 of TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae

description: Additional file 7: Table S4. Tables 1-7 contain the results of the comparative analyses of transcriptomes of ungerminated spores and spores transferred to ‘YPD + rapamycin’ after 0, 10, 30, 60, 120, 240 and 360 minutes following transfer into YPD in the appropriately labelled worksheets All worksheets have the results of the differential transcriptomic analysis in which the values of logFC (FC = fold-change in transcript levels) along with the corresponding logCPM (counts per million), False Discovery Rate (FDR) and P-values are indicated for each gene.
DOI: 10.6084/m9.figshare.14552025.v1
title: Additional file 2 of Evidence for antifouling biocides as one of the limiting factors for the recovery of macrophyte communities in lakes of Schleswig-Holstein

description: Additional file 2. Additional_Information_Machate (2021).
DOI: 10.6084/m9.figshare.14552025
title: Additional file 2 of Evidence for antifouling biocides as one of the limiting factors for the recovery of macrophyte communities in lakes of Schleswig-Holstein

description: Additional file 2. Additional_Information_Machate (2021).
DOI: 10.6084/m9.figshare.14552021
title: Additional file 1 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 1: Table S1. List and information of 1047 A. thaliana accessions included in the study.
DOI: 10.6084/m9.figshare.14552021.v1
title: Additional file 1 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 1: Table S1. List and information of 1047 A. thaliana accessions included in the study.
DOI: 10.6084/m9.figshare.14552024
title: Additional file 2 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 2: Dataset S1. List of 23,331 TIPs and their presence (1) or absence (0) across 1047 accessions.
DOI: 10.6084/m9.figshare.14552024.v1
title: Additional file 2 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 2: Dataset S1. List of 23,331 TIPs and their presence (1) or absence (0) across 1047 accessions.
DOI: 10.6084/m9.figshare.14552030
title: Additional file 4 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 4: Table S2. Results of generalized linear models of recent transposition based on genetic factors.
DOI: 10.6084/m9.figshare.14552030.v1
title: Additional file 4 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 4: Table S2. Results of generalized linear models of recent transposition based on genetic factors.
DOI: 10.6084/m9.figshare.14552033
title: Additional file 5 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 5: Dataset S2. List of 154 transposition events identified in 1000 offspring of WT and nrpd1 parents of the Col-0 accession grown under standard conditions and their presence (1) or absence (0) across both samples.
DOI: 10.6084/m9.figshare.14552033.v1
title: Additional file 5 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 5: Dataset S2. List of 154 transposition events identified in 1000 offspring of WT and nrpd1 parents of the Col-0 accession grown under standard conditions and their presence (1) or absence (0) across both samples.
DOI: 10.6084/m9.figshare.14552036.v1
title: Additional file 6 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 6: Dataset S3. List of 331 transposition events identified in 1000 offspring the Cvi-0, Sha-0, Tsu-0 and Col-0 accessions derived from parents grown under standard conditions grown under standard conditions and their presence (1) or absence (0) across samples.
DOI: 10.6084/m9.figshare.14552039
title: Additional file 7 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 7: Table S3. Results of generalized linear models of recent transposition based on genetic and environmental factors.
DOI: 10.6084/m9.figshare.14552039.v1
title: Additional file 7 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 7: Table S3. Results of generalized linear models of recent transposition based on genetic and environmental factors.
DOI: 10.6084/m9.figshare.14552042
title: Additional file 8 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 8: Dataset S4. List of 189 transposition events identified in 1000 offspring of Col-0 WT and nrpd1 parents grown under standard conditions or exposed to heat-shock or flagellin and their presence (1) or absence (0) across both samples.
DOI: 10.6084/m9.figshare.14552045
title: Additional file 9 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 9: Table S4. List of publicly available RNA-seq datasets used for transcriptomic analyses.
DOI: 10.6084/m9.figshare.14552042.v1
title: Additional file 8 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 8: Dataset S4. List of 189 transposition events identified in 1000 offspring of Col-0 WT and nrpd1 parents grown under standard conditions or exposed to heat-shock or flagellin and their presence (1) or absence (0) across both samples.
DOI: 10.6084/m9.figshare.14552036
title: Additional file 6 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 6: Dataset S3. List of 331 transposition events identified in 1000 offspring the Cvi-0, Sha-0, Tsu-0 and Col-0 accessions derived from parents grown under standard conditions grown under standard conditions and their presence (1) or absence (0) across samples.
DOI: 10.6084/m9.figshare.14552045.v1
title: Additional file 9 of Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana

description: Additional file 9: Table S4. List of publicly available RNA-seq datasets used for transcriptomic analyses.
DOI: 10.6084/m9.figshare.14552054
title: Additional file 2 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 2 This table reports the performance of mLinker solve using haplotype linkage in the RPE-1 linked reads data. For each round of minimization, the following numbers are reported: number of spin flips (column 1), number of block switches (column 2), CPU clock time of spin flipping (column 3) and block switching (column 4), and the maximum residual block-switching energy penalty (column 5). Details of the minimization procedure is provided in Additional file 1:Solving haplotype phase by minimization; spin flipping and block switching are defined in Eqs. (18) and (19).
DOI: 10.6084/m9.figshare.14552054.v1
title: Additional file 2 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 2 This table reports the performance of mLinker solve using haplotype linkage in the RPE-1 linked reads data. For each round of minimization, the following numbers are reported: number of spin flips (column 1), number of block switches (column 2), CPU clock time of spin flipping (column 3) and block switching (column 4), and the maximum residual block-switching energy penalty (column 5). Details of the minimization procedure is provided in Additional file 1:Solving haplotype phase by minimization; spin flipping and block switching are defined in Eqs. (18) and (19).
DOI: 10.6084/m9.figshare.14552060
title: Additional file 3 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 3 This table summarizes additional benchmark metrics of the haplotype solution of the NA12878 genome in comparison to the haplotype phase derived from parental genome sequencing. The parental haplotype data used for comparison include the reference haplotype data released by the Genome-In-A-Bottle consortium (“trio phase”), and phased haplotypes derived from de novo diploid assembly of the NA12878 genome (“dip assembly”) using PacBio CCS reads of the NA12878 genome and short reads of the parental genomes. See Table 1 for more details about the reference haplotype data. In the 1st Tab, each row summarizes the following metrics about the haplotype solution of each chromosome (column 1): phased sites from de novo diploid assembly (column 2), phased sites in the GIAB release (column 3), phased sites in the final unfiltered haplotype solution from mLinker (column 4), phased genotypes in the mLinker solution that are in agreement with the GIAB data (column 5), mLinker phased genotypes in discordance with the GIAB data (column 6), mLinker phased genotypes in agreement with the haplotype from diploid assembly (column 7), mLinker phased genotypes in discordance with the haplotype from diploid assembly (column 8), phased sites in the final filtered haplotype solution from mLinker (column 9), mLinker phased genotypes in agreement with the GIAB data (column 10), mLinker phased genotypes in discordance with the GIAB data (column 11), mLinker phased genotypes in agreement with the haplotype from diploid assembly (column 12), mLinker phased genotypes in discordance with the haplotype from diploid assembly (column 13). The 2nd Tab reports results of the comparison of mLinker-phased genotypes on each parental chromosome with parent-specific sequences derived from the short-read sequencing data of parental genomes. For details about this comparison, see Additional file 1:Comparison of phased variant genotypes with parent-specific k-mer’s.
DOI: 10.6084/m9.figshare.14552063.v1
title: Additional file 4 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 4 This table contains multiple tabs. Tab 1 reports results from the comparison of the mLinker haplotype solution of the RPE-1 genome generated from 60 × linked-reads and Hi-C sequencing data to the reference haplotype data derived from sequencing of monosomic chromosomes. Tabs 2-5 report results from the comparison of the mLinker haplotype resolution generated from downsampled linked-reads and Hi-C data. Tab 6 reports benchmark metrics of the mLinker haplotype solution generated from 11 × PacBio HiFi data and Hi-C data. In Tab 1, the comparison is performed on both the scaffold haplotype solution and the final haplotype solution filtered by haplotype linkage. In Tabs 2-5, the comparison is only performed on the scaffold haplotype solution. For each mLinker solution in Tabs 1-5, we report results from the comparison of phased genotypes at all phased variant sites (“No filter”), at phased sites not in centromeric/acrocentric regions (“Excluding centromere”), and at phased sites also passing the allele fraction filter from single-cell data (“allele filter from single-cell data”). In Tab 6, we report results from two separate calculations, the first using all variants as input, the second using only high-quality variants (sites that pass the linkage filter in the mLinker final haplotype solution derived from linked-reads and Hi-C data). The comparison in Tab 6 is only performed on high-quality variants.
DOI: 10.6084/m9.figshare.14552060.v1
title: Additional file 3 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 3 This table summarizes additional benchmark metrics of the haplotype solution of the NA12878 genome in comparison to the haplotype phase derived from parental genome sequencing. The parental haplotype data used for comparison include the reference haplotype data released by the Genome-In-A-Bottle consortium (“trio phase”), and phased haplotypes derived from de novo diploid assembly of the NA12878 genome (“dip assembly”) using PacBio CCS reads of the NA12878 genome and short reads of the parental genomes. See Table 1 for more details about the reference haplotype data. In the 1st Tab, each row summarizes the following metrics about the haplotype solution of each chromosome (column 1): phased sites from de novo diploid assembly (column 2), phased sites in the GIAB release (column 3), phased sites in the final unfiltered haplotype solution from mLinker (column 4), phased genotypes in the mLinker solution that are in agreement with the GIAB data (column 5), mLinker phased genotypes in discordance with the GIAB data (column 6), mLinker phased genotypes in agreement with the haplotype from diploid assembly (column 7), mLinker phased genotypes in discordance with the haplotype from diploid assembly (column 8), phased sites in the final filtered haplotype solution from mLinker (column 9), mLinker phased genotypes in agreement with the GIAB data (column 10), mLinker phased genotypes in discordance with the GIAB data (column 11), mLinker phased genotypes in agreement with the haplotype from diploid assembly (column 12), mLinker phased genotypes in discordance with the haplotype from diploid assembly (column 13). The 2nd Tab reports results of the comparison of mLinker-phased genotypes on each parental chromosome with parent-specific sequences derived from the short-read sequencing data of parental genomes. For details about this comparison, see Additional file 1:Comparison of phased variant genotypes with parent-specific k-mer’s.
DOI: 10.6084/m9.figshare.14552069.v1
title: Additional file 6 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 6 Each row in this table corresponds to a monosomy (column 2) in a single cell sample (column 1). The following metrics are reported for each monosomy: mean sequencing depth of the monosomic chromosome (column 3) and across the genome (column 4), percentage of reference (column 5), alternate (column 6), and heterozygous coverage (column 7), normalized heterozygosity (column 8), SRA BioProject ID (column 9), SRR accession number (column 10). Details of data generation and analysis are provided in “Sequencing data of monosomic RPE-1 cells” section.
DOI: 10.6084/m9.figshare.14552069
title: Additional file 6 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 6 Each row in this table corresponds to a monosomy (column 2) in a single cell sample (column 1). The following metrics are reported for each monosomy: mean sequencing depth of the monosomic chromosome (column 3) and across the genome (column 4), percentage of reference (column 5), alternate (column 6), and heterozygous coverage (column 7), normalized heterozygosity (column 8), SRA BioProject ID (column 9), SRR accession number (column 10). Details of data generation and analysis are provided in “Sequencing data of monosomic RPE-1 cells” section.
DOI: 10.6084/m9.figshare.14552063
title: Additional file 4 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 4 This table contains multiple tabs. Tab 1 reports results from the comparison of the mLinker haplotype solution of the RPE-1 genome generated from 60 × linked-reads and Hi-C sequencing data to the reference haplotype data derived from sequencing of monosomic chromosomes. Tabs 2-5 report results from the comparison of the mLinker haplotype resolution generated from downsampled linked-reads and Hi-C data. Tab 6 reports benchmark metrics of the mLinker haplotype solution generated from 11 × PacBio HiFi data and Hi-C data. In Tab 1, the comparison is performed on both the scaffold haplotype solution and the final haplotype solution filtered by haplotype linkage. In Tabs 2-5, the comparison is only performed on the scaffold haplotype solution. For each mLinker solution in Tabs 1-5, we report results from the comparison of phased genotypes at all phased variant sites (“No filter”), at phased sites not in centromeric/acrocentric regions (“Excluding centromere”), and at phased sites also passing the allele fraction filter from single-cell data (“allele filter from single-cell data”). In Tab 6, we report results from two separate calculations, the first using all variants as input, the second using only high-quality variants (sites that pass the linkage filter in the mLinker final haplotype solution derived from linked-reads and Hi-C data). The comparison in Tab 6 is only performed on high-quality variants.
DOI: 10.6084/m9.figshare.14552072
title: Additional file 7 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 7 Please refer to Whole-chromosome haplotype inference by HapCUT2 for a detailed explanation.
DOI: 10.6084/m9.figshare.14552072.v1
title: Additional file 7 of Determination of complete chromosomal haplotypes by bulk DNA sequencing

description: Additional file 7 Please refer to Whole-chromosome haplotype inference by HapCUT2 for a detailed explanation.
DOI: 10.6084/m9.figshare.14552079
title: Additional file 2 of Carotid endarterectomy with patch angioplasty versus primary closure in patients with symptomatic and significant stenosis: a systematic review with meta-analyses and trial sequential analysis of randomized clinical trials

description: Additional file 2. GRADE summary of findings table.
DOI: 10.6084/m9.figshare.14552079.v1
title: Additional file 2 of Carotid endarterectomy with patch angioplasty versus primary closure in patients with symptomatic and significant stenosis: a systematic review with meta-analyses and trial sequential analysis of randomized clinical trials

description: Additional file 2. GRADE summary of findings table.
DOI: 10.6084/m9.figshare.14552105.v1
title: Additional file 1 of Clinical exome sequencing facilitates the understanding of genetic heterogeneity in Leber congenital amaurosis patients with variable phenotype in southern India

description: Additional file 1: Supplementary Table S1. Primer sequences used for the mutation validation by Sanger sequencing.
DOI: 10.6084/m9.figshare.14552108.v1
title: Additional file 2 of Clinical exome sequencing facilitates the understanding of genetic heterogeneity in Leber congenital amaurosis patients with variable phenotype in southern India

description: Additional file 2: Supplementary Table S2. Summary of clinical exome data.
DOI: 10.6084/m9.figshare.14552105
title: Additional file 1 of Clinical exome sequencing facilitates the understanding of genetic heterogeneity in Leber congenital amaurosis patients with variable phenotype in southern India

description: Additional file 1: Supplementary Table S1. Primer sequences used for the mutation validation by Sanger sequencing.
DOI: 10.6084/m9.figshare.14552108
title: Additional file 2 of Clinical exome sequencing facilitates the understanding of genetic heterogeneity in Leber congenital amaurosis patients with variable phenotype in southern India

description: Additional file 2: Supplementary Table S2. Summary of clinical exome data.
DOI: 10.6084/m9.figshare.14552114
title: Additional file 3 of Clinical exome sequencing facilitates the understanding of genetic heterogeneity in Leber congenital amaurosis patients with variable phenotype in southern India

description: Additional file 3: Supplementary Table S3. Overview of exclusion and prioritization of variants to obtain pathogenic variant from clinical exome data.