cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7010819
title: Additional file 5: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: Heatmap of all Gene Ontology (GO) terms. Table showing distribution of various GO categories across cell-type clusters. (XLSX 2009 kb)
DOI: 10.6084/m9.figshare.7010822.v1
title: Additional file 6: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: Distribution of significantly upregulated/downregulated enzymes in the clusters. Table indicating pathways displaying patterns of significantly upregulated or downregulated enzymes. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7010816
title: Additional file 4: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: Distribution of predicted transcription factors in clusters. Three tables indicating distribution of transcription factors identified in the Toronto transcriptome with clusters identified by Seurat. (XLSX 4752 kb)
DOI: 10.6084/m9.figshare.7010819.v1
title: Additional file 5: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: Heatmap of all Gene Ontology (GO) terms. Table showing distribution of various GO categories across cell-type clusters. (XLSX 2009 kb)
DOI: 10.6084/m9.figshare.7010813
title: Additional file 3: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: List of predicted transcription factors identified in Toronto transcriptome dataset. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.7010816.v1
title: Additional file 4: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: Distribution of predicted transcription factors in clusters. Three tables indicating distribution of transcription factors identified in the Toronto transcriptome with clusters identified by Seurat. (XLSX 4752 kb)
DOI: 10.6084/m9.figshare.7010813.v1
title: Additional file 3: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: List of predicted transcription factors identified in Toronto transcriptome dataset. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.7010798
title: Additional file 1: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: Characteristics of the Toronto definitive transcriptome. Details of S. mediterranea transcripts in the definitive transcriptome. (XLSB 18937 kb)
DOI: 10.6084/m9.figshare.7010798.v1
title: Additional file 1: of Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

description: Characteristics of the Toronto definitive transcriptome. Details of S. mediterranea transcripts in the definitive transcriptome. (XLSB 18937 kb)
DOI: 10.6084/m9.figshare.7010792
title: Additional file 1: of Pharm-MD; an open-label, randomized controlled, phase II study to evaluate the efficacy of a pharmacist-managed diabetes clinic in high-risk diabetes patients â study protocol for a randomized controlled trial

description: Institutional Review Board (IRB)-approved informed consent; outcome letter with IRB approval; grant award letter; pharmacy visit template; standard of care (SOC) appointment card; standard of care + pharmacist-managed diabetes clinic (SOC + PMDC) appointment card; pharmacy appointment card; Diabetes-39 questionnaire. (ZIP 443 kb)
DOI: 10.6084/m9.figshare.7010792.v1
title: Additional file 1: of Pharm-MD; an open-label, randomized controlled, phase II study to evaluate the efficacy of a pharmacist-managed diabetes clinic in high-risk diabetes patients â study protocol for a randomized controlled trial

description: Institutional Review Board (IRB)-approved informed consent; outcome letter with IRB approval; grant award letter; pharmacy visit template; standard of care (SOC) appointment card; standard of care + pharmacist-managed diabetes clinic (SOC + PMDC) appointment card; pharmacy appointment card; Diabetes-39 questionnaire. (ZIP 443 kb)
DOI: 10.6084/m9.figshare.7010777
title: Additional file 2: of Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

description: Supplementary material containing OTU table, list of corresponding reference sequence for each OTU, and sample metadata. (ZIP 946 kb)
DOI: 10.6084/m9.figshare.7010777.v1
title: Additional file 2: of Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

description: Supplementary material containing OTU table, list of corresponding reference sequence for each OTU, and sample metadata. (ZIP 946 kb)
DOI: 10.6084/m9.figshare.7010768
title: Additional file 9: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Drug Sensitivity Scores [42] of CTG measurement and cell count. Max.Conc [nM] = maximum concentration, Min.Conc [nM] = minimum concentration, MAX = maximum % inhibition, D1 [% inhibition]… D5 [% inhibition] = % inhibition from the lowest (D1) to the highest drug concentration (D5). (XLSX 27 kb)
DOI: 10.6084/m9.figshare.7010768.v1
title: Additional file 9: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Drug Sensitivity Scores [42] of CTG measurement and cell count. Max.Conc [nM] = maximum concentration, Min.Conc [nM] = minimum concentration, MAX = maximum % inhibition, D1 [% inhibition]… D5 [% inhibition] = % inhibition from the lowest (D1) to the highest drug concentration (D5). (XLSX 27 kb)
DOI: 10.6084/m9.figshare.7010756
title: Additional file 8: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Enriched pathways with adjusted p
DOI: 10.6084/m9.figshare.7010756.v1
title: Additional file 8: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Enriched pathways with adjusted p
DOI: 10.6084/m9.figshare.7010723
title: Additional file 7: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Batch corrected CPM counts of cell lines and patients. (TXT 28313 kb)
DOI: 10.6084/m9.figshare.7010723.v1
title: Additional file 7: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Batch corrected CPM counts of cell lines and patients. (TXT 28313 kb)
DOI: 10.7284/107360
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN493 using a Furuno GP-90D instrument system onboard the platform RV Endeavor
DOI: 10.6084/m9.figshare.7010711
title: Additional file 6: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Detected fusion genes of parental and tamoxifen-resistant cell lines. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.7010708
title: Additional file 6: of Interaction between the microbiome and TP53 in human lung cancer

description: Clinical metadata and taxa IDs for TCGA samples. (XLSX 17974 kb)
DOI: 10.6084/m9.figshare.7010711.v1
title: Additional file 6: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Detected fusion genes of parental and tamoxifen-resistant cell lines. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.7010708.v1
title: Additional file 6: of Interaction between the microbiome and TP53 in human lung cancer

description: Clinical metadata and taxa IDs for TCGA samples. (XLSX 17974 kb)
DOI: 10.18462/iir.rankine.2020.1128
title: Fast calculation method for performance upper-limit of (quasi) two-stage vapour compression system.
DOI: 10.6084/m9.figshare.7010690
title: Additional file 5: of Interaction between the microbiome and TP53 in human lung cancer

description: Clinical metadata and OTUs for NCI-MD samples. (XLSX 808 kb)
DOI: 10.6084/m9.figshare.7010690.v1
title: Additional file 5: of Interaction between the microbiome and TP53 in human lung cancer

description: Clinical metadata and OTUs for NCI-MD samples. (XLSX 808 kb)
DOI: 10.6084/m9.figshare.7010687
title: Additional file 4: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: RNA-sequencing statistics. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7010687.v1
title: Additional file 4: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: RNA-sequencing statistics. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7010678
title: Additional file 3: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Statistical analysis of triglycerides, free cholesterol and cholesterol esters, LMP assay, and LipidToxGreen staining. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7010678.v1
title: Additional file 3: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Statistical analysis of triglycerides, free cholesterol and cholesterol esters, LMP assay, and LipidToxGreen staining. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7010666
title: Additional file 2: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Drugs used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7010669
title: Additional file 4: of Interaction between the microbiome and TP53 in human lung cancer

description: Distribution of samples across runs of 16S rRNA sequencing. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7010666.v1
title: Additional file 2: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Drugs used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7010669.v1
title: Additional file 4: of Interaction between the microbiome and TP53 in human lung cancer

description: Distribution of samples across runs of 16S rRNA sequencing. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7010663
title: Additional file 1: of Hyaluronan–binding protein 2 (HABP2) gene variation in women with recurrent miscarriage

description: SNP raw data for cases and controls is shown. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7010663.v1
title: Additional file 1: of Hyaluronan–binding protein 2 (HABP2) gene variation in women with recurrent miscarriage

description: SNP raw data for cases and controls is shown. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7010657
title: Additional file 1: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Antibodies used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7010657.v1
title: Additional file 1: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Antibodies used in this study. (XLSX 10 kb)
DOI: 10.7284/107227
title: Multiplexed data collected during research cruise EN498 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor
DOI: 10.6084/m9.figshare.7010651
title: Additional file 3: of Interaction between the microbiome and TP53 in human lung cancer

description: Background contamination swabs and relative abundance. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.7010645
title: Additional file 10: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Mean of the mean LipidToxGreen intensity values. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.7010645.v1
title: Additional file 10: of Association of tamoxifen resistance and lipid reprogramming in breast cancer

description: Mean of the mean LipidToxGreen intensity values. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.7010651.v1
title: Additional file 3: of Interaction between the microbiome and TP53 in human lung cancer

description: Background contamination swabs and relative abundance. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.7010495
title: Supplemental figures and files for "Assessment of genetic differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers."

description: <b>Figure S1</b><b>. The cross-validation error of K value in ADMIXTURE. </b>This figure shows the cross-validation of ADMIXTURE for the 98 <i>S. pimpinellifolium</i> accessions. The lowest cross-validation error is best K = 3. <b>Figure S2.</b><b> LD decay of the whole genome. </b>The pairwise LD through the whole genome was plotted. The red curve indicates non-linear regression. The dotted line indicates the fixed <i>r<sup>2</sup></i> on 0.1.<br> <b>Figure S3. 50 kb interval LD decay of each chromosome. </b>The pairwise LD of each chromosome was plotted individually and zoomed in to 50 kb interval to observe the fast LD decay. The red curves indicate non-linear regression. Black dotted lines indicate the fixed <i>r<sup>2</sup></i> on 0.1. <b>Figure S4. The local LD of each chromosome. </b>The LD of paired flanking sequencing units were plotted along each chromosome. The red dotted line indicates the baseline of <i>r<sup>2</sup></i>, and the orange line indicates the heterochromatic region. <b>Figure S5.</b><b> Pairwise isolation by distance of 98 accessions. </b>This plot presents the correlation between pairwise genetic distance and geographic distance. <b>Figure S6.</b><b> Pairwise isolation by distance of SolCAP meta-analysis. </b>This plot presents the correlation between pairwise genetic distance and geographic distance for the collection of 214 samples from the previous studies (Blanca <i>et al.</i> 2012, 2015; Sim <i>et al.</i> 2012a). <b>Figure S7.</b><b> The cross-validation error of SolCAP meta-analysis. </b>This figure shows the cross-validation of ADMIXTURE analysis for the SolCAP genotypes of the 214 <i>S. pimpinellifolium</i> accessions in the previous studies (Blanca <i>et al.</i> 2012, 2015; Sim <i>et al.</i> 2012a). The lowest cross-validation error shows best K = 15. <b>Figure S8. The genome patterns of 214 samples in SolCAP meta-analysis. </b>The labels on the top indicate accessions; the labels on the bottom indicate sample ID in this meta-analysis. <b>Figure S9.</b><b> The PCA of SolCAP meta-analysis. </b>A) The PCA plot of bi-allelic SNPs. B) The PCA plot after removing those SNPs of reverse-complement allele designation.<b>File S1. The analysis of isolation by distance. </b>The isolation by distance was performed for the 98 <i>S. pimpinellifolium</i> accessions with the RAD SNP dataset.<b>File S2. </b><b>The meta-analysis of <i>S. pimpinellifolium</i> SolCAP genotyping data. </b>We performed a meta-analysis of 214 <i>S. pimpinellifolium</i> accessions using SolCAP genotyping data downloaded from previous studies Sim <i>et al.</i> 2012a, Blanca <i>et al.</i> 2012, and Blanca <i>et al.</i> 2015.<br>
DOI: 10.6084/m9.figshare.7010492
title: Supplemental tables for "Assessment of genetic differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers"

description: <b>Table S1. The detail information of each accession. </b>This table lists the RAD sequencing summary, mating type and collection location of the 99 <i>S. pimpinellifolium</i> in this study. The RAD sequencing summary includes the reads, the missing proportion and the heterozygous proportion. FSC and ASC indicate facultative self-compatible and autogamous self-compatible mating type, respectively. <b>Table S2. The statistical summaries of expected sites and sequenced sites of <i>Pst</i>I, the sites targeted by SNP and the sequenced genes. </b>This table contains the numbers of expected cutting sites and the actually sequenced sites of <i>Pst</i>I of each chromosome in this study. The sequenced sites are also checked if they contained any SNP. The number of expected genes in the expected sequencing regions is summarized to reveal the capability of capturing genes in this RAD sequencing strategy. Also, the sequenced genes are summarized.<br> <b>Table S3. The information of 24,330 SNPs. </b>We list all the genotypes of the 98 <i>S. pimpinellifolium</i>. Each row indicates a SNP and each column indicates an individual. <b>Table S4. Pairwise F<sub>st </sub>of seven subpopulations. </b>This table is the pairwise F<sub>st</sub> of seven subpopulations for 98 <i>S. pimpinellifolium</i>. The names of subpopulations are stated in Table 2. <b>Table S5. The locations and genotypes of 214 samples of SolCAP genotyping array. </b>This table contains the 2,307 consistent allele calling markers of SolCAP array for 214 samples in the three previous studies (Blanca <i>et al.</i> 2012, 2015; Sim <i>et al.</i> 2012a). The gathering locations are also provided. <b>Table S6. The removed 627 SNPs with reverse-complement allele designation. </b>This list includes the SNPs we removed in SolCAP meta-analysis due to reverse-complement allele designation <b>Table S7. The identity of 2,307 SNP markers within accessions. </b>For the 214 <i>S. pimpinellifolium</i>, we listed all the accessions that contain more than one individual to count monomorphic SNP. The identity is the percentage of monomorphic SNP for the same accession excluding missing values.
DOI: 10.6084/m9.figshare.7010492.v2
title: Supplemental tables for "Assessment of genetic differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers"

description: <b>Table S1. The detail information of each accession. </b>This table lists the RAD sequencing summary, mating type and collection location of the 99 <i>S. pimpinellifolium</i> in this study. The RAD sequencing summary includes the reads, the missing proportion and the heterozygous proportion. FSC and ASC indicate facultative self-compatible and autogamous self-compatible mating type, respectively. <b>Table S2. The statistical summaries of expected sites and sequenced sites of <i>Pst</i>I, the sites targeted by SNP and the sequenced genes. </b>This table contains the numbers of expected cutting sites and the actually sequenced sites of <i>Pst</i>I of each chromosome in this study. The sequenced sites are also checked if they contained any SNP. The number of expected genes in the expected sequencing regions is summarized to reveal the capability of capturing genes in this RAD sequencing strategy. Also, the sequenced genes are summarized.<br> <b>Table S3. The information of 24,330 SNPs. </b>We list all the genotypes of the 98 <i>S. pimpinellifolium</i>. Each row indicates a SNP and each column indicates an individual. <b>Table S4. Pairwise F<sub>st </sub>of seven subpopulations. </b>This table is the pairwise F<sub>st</sub> of seven subpopulations for 98 <i>S. pimpinellifolium</i>. The names of subpopulations are stated in Table 2. <b>Table S5. The locations and genotypes of 214 samples of SolCAP genotyping array. </b>This table contains the 2,307 consistent allele calling markers of SolCAP array for 214 samples in the three previous studies (Blanca <i>et al.</i> 2012, 2015; Sim <i>et al.</i> 2012a). The gathering locations are also provided. <b>Table S6. The removed 627 SNPs with reverse-complement allele designation. </b>This list includes the SNPs we removed in SolCAP meta-analysis due to reverse-complement allele designation <b>Table S7. The identity of 2,307 SNP markers within accessions. </b>For the 214 <i>S. pimpinellifolium</i>, we listed all the accessions that contain more than one individual to count monomorphic SNP. The identity is the percentage of monomorphic SNP for the same accession excluding missing values.
DOI: 10.6084/m9.figshare.7010492.v1
title: Supplemental tables for "Assessment of population differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers"

description: <b>Table S1. The detail information of each accession. </b> This table lists the RAD sequencing summary, mating type and collection location of the 99 <i>S. pimpinellifolium</i> in this study. The RAD sequencing summary includes the reads, the missing proportion and the heterozygous proportion. FSC and ASC indicate facultative self-compatible and autogamous self-compatible mating type, respectively.<br> <b>Table S2. The expected sites and sequenced sites of <i>Pst</i>I as well as the sites with SNP. </b> This table contains the numbers of expected cutting sites and the actually sequenced sites of <i>Pst</i>I of each chromosome in this study. The sequenced sites are also checked if they contained any SNP. The number of expected genes in the expected sequencing regions is listed to reveal the capability of capturing genes in this RAD sequencing strategy.<br> <b>Table S3. The information of 24,330 SNPs. </b> We list all the genotypes of the 98 <i>S. pimpinellifolium</i>. Each row indicates a single SNP and each column indicates an individual.<br> <b>Table S4. The list of InDel markers. </b>The putative InDel markers are summarized in this table, including the physical positions, reference alleles and Insertion/Deletion alleles.<br> <b>Table S5. The list of SSR markers. </b>The putative SSR markers are summarized in this table. The SSR markers were obtained from the InDel markers if the InDels show tandem repeat units. The physical positions, repeat units and the InDel length are listed.<br> <b>Table S6. Pair-wise F<sub>st</sub> of subpopulations. </b>This table is the pair-wise F<sub>st</sub> result of seven subpopulations of 98 <i>S. pimpinellifolium</i>. The blue, red and green groups are the three pure ancestries in ADMIXTURE result. The blue-green, red-blue and red-green groups are the admixture groups of pair ancestries. Three-mixture indicates the group contains the three ancestries.<br> <b>Table S7. The genotypes of 4,326 SNPs of 214 samples. </b>This table contains the bi-allelic genotypes of SolCAP array of 214 <i>S. pimpinellifolium</i> in the three previous studies (Sim et al., 2012; Blanca et al., 2012; Blanca et al., 2015). The ID was labelled by the accession and its original study. Each row indicates a single SNP and each column indicates an individual.<br> <b>Table S8. The identity of 4,326 SNPs within accessions. </b>For the 214 <i>S. pimpinellifolium</i>, we listed all the accessions whose sample size is more than one individual and checked the number of monomorphic SNP. The identity is the percentage of monomorphic SNP within the same accession excluding missing values.