cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14379219.v1
title: Additional file 2 of Complex interactions of lovastatin with 10 chemotherapeutic drugs: a rigorous evaluation of synergism and antagonism

description: Additional file 2: Legends Figure S1. Schematic diagram of the 96-well plate for the dual-drug assays (see Methods). The dose-responses (Columns 9 and 10), which are required for the computation of Loewe additive synergy, are performed at the same starting concentrations and with the same dilutions as in the dual-dilution portion of the plate. The format shown is compatible with the Combenefit software. BL = Plate blank (synthetic complete media + dextrose only). Figure S2. Tamoxifen plus lovastatin data on day 3. The comparable data for day two are depicted and described in Figure 2. The synergy matrix shown here is very similar to the day two matrix. Figure S3. Doxorubicin and lovastatin interactions on day three. The data are quite similar to the results on day two, shown in Figure 3. Figure S4. Methotrexate and lovastatin on day three. The patterns are quite similar to those recorded on day two (Fig. 4). The Loewe synergy matrix (D) is the same plot as shown in Fig. 4e. Figure S5. Experimental dose-response data for the combination of rapamycin and lovastatin. The combination dose-response data are visualized as contours, with 25, 50, 75 and 100% of control levels. Even though the EC50 of rapamycin is three-fold greater on day3 (Fig. 5, d vs. a), the 25% dose-response contour is achievable at all concentrations of rapamycin with only a modest increase in lovastatin concentration compared to day two. These data, supportive of the increase in synergy seen in the Loewe matrix (Fig. 5f compared to c), suggest that lovastatin somehow prolongs the efficacy of rapamycin. Figure S6. Day three Loewe synergy matrices corresponding to the day two data shown in Fig. 6. Epothilone plus lovastatin exhibits significant synergy on day three (C) whereas the combination did not on day two (Fig. 6c). The matrix for 5-fluoruracil (A) shows no significant interactions, as it did on day two. The other four drugs, gemcitabine (B), cisplatin (D), cyclophosphamide (E), and etoposide (F), exhibit greater antagonism on the third day. Figure S7. Loewe synergy matrices on days two and three for three cell lines in dual-drug assays of cisplatin in combination with lovastatin. Two human cancer cells lines, A549 (lung adenocarcinoma) (A, D) and MCF7 (breast cancer) (C, F), exhibited significant antagonism (and no significant synergism) on day two; the antagonism was more pronounced on day three. The HT29 colon adenocarcinoma cell line exhibited synergism and antagonism, both statistically significant, on day two (B) and to a lesser degree, on day three (E). The data shown here are comparable to that obtained with the S. cerevisiae assays (see Table 2, and Figs. 6c and S6D).
DOI: 10.5519/qd.1iwn8r1s
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (822 records)
DOI: 10.6084/m9.figshare.14538771
title: Additional file 2 of Genetic alterations and their therapeutic implications in epithelial ovarian cancer

description: Additional file 2. List of mean sequencing depth and uniformity for all study patients for both cancer panels used in the present study.
DOI: 10.6084/m9.figshare.14538771.v1
title: Additional file 2 of Genetic alterations and their therapeutic implications in epithelial ovarian cancer

description: Additional file 2. List of mean sequencing depth and uniformity for all study patients for both cancer panels used in the present study.
DOI: 10.6084/m9.figshare.14538780
title: Additional file 5 of Genetic alterations and their therapeutic implications in epithelial ovarian cancer

description: Additional file 5. Protein coding and splice mutations observed in all patients included in the present study (n = 82).
DOI: 10.6084/m9.figshare.14538783
title: Additional file 6 of Genetic alterations and their therapeutic implications in epithelial ovarian cancer

description: Additional file 6. Detected mutation and copy number variants in analyzed cancer signaling pathways, and their classification.
DOI: 10.6084/m9.figshare.14538780.v1
title: Additional file 5 of Genetic alterations and their therapeutic implications in epithelial ovarian cancer

description: Additional file 5. Protein coding and splice mutations observed in all patients included in the present study (n = 82).
DOI: 10.6084/m9.figshare.14538783.v1
title: Additional file 6 of Genetic alterations and their therapeutic implications in epithelial ovarian cancer

description: Additional file 6. Detected mutation and copy number variants in analyzed cancer signaling pathways, and their classification.
DOI: 10.6084/m9.figshare.14538797
title: Additional file 2 of Convergence of the turkey gut microbiota following cohabitation under commercial settings

description: Additional file 2. Supplementary Tables S1-S4.
DOI: 10.6084/m9.figshare.14538797.v1
title: Additional file 2 of Convergence of the turkey gut microbiota following cohabitation under commercial settings

description: Additional file 2. Supplementary Tables S1-S4.
DOI: 10.6084/m9.figshare.13939945
title: Additional file 3 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 3: Supplementary Table 1. (1957 Ethylene AZ150 DEGs annotated and expression summary)
DOI: 10.6084/m9.figshare.13939948.v1
title: Additional file 4 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 4: Supplementary Table 2. (502 Tissue comparison DEGs annotated and expression summary)
DOI: 10.6084/m9.figshare.13939951
title: Additional file 5 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 5; Supplementary Table 3. (168 NA vs ET DEGs annotated and expression summary)
DOI: 10.6084/m9.figshare.13939945.v1
title: Additional file 3 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 3: Supplementary Table 1. (1957 Ethylene AZ150 DEGs annotated and expression summary)
DOI: 10.6084/m9.figshare.13939948
title: Additional file 4 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 4: Supplementary Table 2. (502 Tissue comparison DEGs annotated and expression summary)
DOI: 10.6084/m9.figshare.13939951.v1
title: Additional file 5 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 5; Supplementary Table 3. (168 NA vs ET DEGs annotated and expression summary)
DOI: 10.6084/m9.figshare.13939954
title: Additional file 6 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 6: Supplementary Table 4. (qPCR primers used in studies)
DOI: 10.6084/m9.figshare.13939954.v1
title: Additional file 6 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 6: Supplementary Table 4. (qPCR primers used in studies)
DOI: 10.6084/m9.figshare.13939957.v1
title: Additional file 7 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 7: Supplementary Table 5. (23 gene candidates overview of validation and expression)
DOI: 10.6084/m9.figshare.13939960.v1
title: Additional file 8 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 8: Supplementary Table 6. (RPKM global for entire transcriptome during Natural Abscission)
DOI: 10.6084/m9.figshare.13939957
title: Additional file 7 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 7: Supplementary Table 5. (23 gene candidates overview of validation and expression)
DOI: 10.6084/m9.figshare.13939960
title: Additional file 8 of Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission

description: Additional file 8: Supplementary Table 6. (RPKM global for entire transcriptome during Natural Abscission)
DOI: 10.6084/m9.figshare.14538813
title: Additional file 2 of Single-cell sequencing of the small and AT-skewed genome of malaria parasites

description: Additional file 2: Table S1. GC content of 5 base windows in the P. falciparum genome. Table S2. Primer and probe design for droplet digital PCR. Table S3. Correlation between ddPCR gene copy concentration and sequencing depth of ddPCR target. Table S4. Overall sequencing read output and percentage of aligned reads to P. falciparum genome. Table S5. Proportion of reads that contain the MALBAC primer common sequence and their alignment to specific genomic regions. Table S6. CNVs detected by LUMPY in all samples (single cell and Dd2 bulk). Table S7. CNVs detected by Ginkgo in all samples (single cell and Dd2 bulk). Table S8. The number of single cell samples processed at each analysis step. Table S9. DNA yield after MALBAC amplification. Table S10. Primary data from ddPCR detection: calculation of uniformity score and Pfmdr1 copy number. Table S11. Coefficient of variation of normalized read abundance in each sequenced sample. Table S12. The equality of CVs in normalized read abundance for sequenced samples. Table S13. Spearman correlation coefficient of all sequenced samples. Table S14. Comparison between experimental conditions of MALBAC and MDA-amplified single cell samples. Table S15. The coefficient of variation of normalized read abundance in MDA amplified samples. Table S16. Coverage comparison after downsampling to 300,000 reads. Table S17. Spearman correlation coefficient of MDA amplified samples. Table S18. Detection of true CNVs in single cell genomes by discordant/split read or read depth analysis. Table S19. Precision and sensitivity of CNV detection. Table S20. Single cell CNVs detected by both discordant/split read and read depth analysis (excluding true CNVs presented in Table 5). Table S21. Detection of known SNPs in resistant genes in Dd2 bulk sample. Table S22. Detection of known SNPs in resistant genes in single cell samples. Table S23. Subpopulation SNPs detected in single cell samples. Table S24. Pathways of genes affected by novel SNPs detected in single cell samples.
DOI: 10.6084/m9.figshare.14538813.v1
title: Additional file 2 of Single-cell sequencing of the small and AT-skewed genome of malaria parasites

description: Additional file 2: Table S1. GC content of 5 base windows in the P. falciparum genome. Table S2. Primer and probe design for droplet digital PCR. Table S3. Correlation between ddPCR gene copy concentration and sequencing depth of ddPCR target. Table S4. Overall sequencing read output and percentage of aligned reads to P. falciparum genome. Table S5. Proportion of reads that contain the MALBAC primer common sequence and their alignment to specific genomic regions. Table S6. CNVs detected by LUMPY in all samples (single cell and Dd2 bulk). Table S7. CNVs detected by Ginkgo in all samples (single cell and Dd2 bulk). Table S8. The number of single cell samples processed at each analysis step. Table S9. DNA yield after MALBAC amplification. Table S10. Primary data from ddPCR detection: calculation of uniformity score and Pfmdr1 copy number. Table S11. Coefficient of variation of normalized read abundance in each sequenced sample. Table S12. The equality of CVs in normalized read abundance for sequenced samples. Table S13. Spearman correlation coefficient of all sequenced samples. Table S14. Comparison between experimental conditions of MALBAC and MDA-amplified single cell samples. Table S15. The coefficient of variation of normalized read abundance in MDA amplified samples. Table S16. Coverage comparison after downsampling to 300,000 reads. Table S17. Spearman correlation coefficient of MDA amplified samples. Table S18. Detection of true CNVs in single cell genomes by discordant/split read or read depth analysis. Table S19. Precision and sensitivity of CNV detection. Table S20. Single cell CNVs detected by both discordant/split read and read depth analysis (excluding true CNVs presented in Table 5). Table S21. Detection of known SNPs in resistant genes in Dd2 bulk sample. Table S22. Detection of known SNPs in resistant genes in single cell samples. Table S23. Subpopulation SNPs detected in single cell samples. Table S24. Pathways of genes affected by novel SNPs detected in single cell samples.
DOI: 10.6084/m9.figshare.14538816.v1
title: Additional file 3 of Single-cell sequencing of the small and AT-skewed genome of malaria parasites

description: Additional file 3. SNPs detected in all samples. Excel file of SNPs detected in all samples with gene name annotation (VQSLOD &gt; 6).
DOI: 10.6084/m9.figshare.14538819.v1
title: Additional file 4 of Single-cell sequencing of the small and AT-skewed genome of malaria parasites

description: Additional file 4. Single cell novel SNPs. Excel file of Single cell novel SNPs with gene name annotation (VQSLOD &gt; 6, DP &gt; 10).
DOI: 10.6084/m9.figshare.14538819
title: Additional file 4 of Single-cell sequencing of the small and AT-skewed genome of malaria parasites

description: Additional file 4. Single cell novel SNPs. Excel file of Single cell novel SNPs with gene name annotation (VQSLOD &gt; 6, DP &gt; 10).
DOI: 10.6084/m9.figshare.14538816
title: Additional file 3 of Single-cell sequencing of the small and AT-skewed genome of malaria parasites

description: Additional file 3. SNPs detected in all samples. Excel file of SNPs detected in all samples with gene name annotation (VQSLOD &gt; 6).
DOI: 10.6084/m9.figshare.14538885
title: Additional file 1 of Genome-wide histone acetylation analysis reveals altered transcriptional regulation in the Parkinson’s disease brain

description: Additional file 1.
DOI: 10.6084/m9.figshare.14538885.v1
title: Additional file 1 of Genome-wide histone acetylation analysis reveals altered transcriptional regulation in the Parkinson’s disease brain

description: Additional file 1.
DOI: 10.6084/m9.figshare.14006173
title: Additional file 3 of Lipid profile of Mexican children with Down syndrome

description: Additional file 3.
DOI: 10.6084/m9.figshare.14006173.v1
title: Additional file 3 of Lipid profile of Mexican children with Down syndrome

description: Additional file 3.
DOI: 10.6084/m9.figshare.14538930
title: Additional file 1 of First Nations emergency care in Alberta: descriptive results of a retrospective cohort study

description: Additional file 1: Appendices 1-4. 1. EDC Groupings used in Analysis. Appendix 2. Day of Week by Shift (Night, Day, Evening). Appendix 3. Emergency visit comorbidities. Appendix 4. Unique Patient Variables (based on 1st emergency visit).
DOI: 10.6084/m9.figshare.14538930.v1
title: Additional file 1 of First Nations emergency care in Alberta: descriptive results of a retrospective cohort study

description: Additional file 1: Appendices 1-4. 1. EDC Groupings used in Analysis. Appendix 2. Day of Week by Shift (Night, Day, Evening). Appendix 3. Emergency visit comorbidities. Appendix 4. Unique Patient Variables (based on 1st emergency visit).
DOI: 10.6084/m9.figshare.14538938.v1
title: Additional file 1 of Benefit of replanning in MR-guided online adaptive radiation therapy in the treatment of liver metastasis

description: Additional file 1. Adaptive volume changes of GTV and PTV.
DOI: 10.6084/m9.figshare.14538938
title: Additional file 1 of Benefit of replanning in MR-guided online adaptive radiation therapy in the treatment of liver metastasis

description: Additional file 1. Adaptive volume changes of GTV and PTV.
DOI: 10.6084/m9.figshare.14059988
title: Additional file 6 of Evaluation of a clinical decision support system for rare diseases: a qualitative study

description: Additional file 6. Results of the questionnaire.
DOI: 10.6084/m9.figshare.14059988.v1
title: Additional file 6 of Evaluation of a clinical decision support system for rare diseases: a qualitative study

description: Additional file 6. Results of the questionnaire.
DOI: 10.6084/m9.figshare.14037842
title: Additional file 1 of Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene

description: Additional file 1: Table S1. Sample identification, localities, haplotypes designation, and the GenBank Accession Numbers for each of the samples used in this study.
DOI: 10.6084/m9.figshare.14037842.v1
title: Additional file 1 of Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene

description: Additional file 1: Table S1. Sample identification, localities, haplotypes designation, and the GenBank Accession Numbers for each of the samples used in this study.
DOI: 10.6084/m9.figshare.14037845
title: Additional file 2 of Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene

description: Additional file 2: Table S2. Species, sample identification, localities, haplotypes designation, and the GenBank Accession Numbers for downloaded sequences from GenBank used in this study.
DOI: 10.6084/m9.figshare.14037845.v1
title: Additional file 2 of Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene

description: Additional file 2: Table S2. Species, sample identification, localities, haplotypes designation, and the GenBank Accession Numbers for downloaded sequences from GenBank used in this study.
DOI: 10.6084/m9.figshare.14168584.v1
title: Additional file 1 of Six months in: pandemic crime trends in England and Wales

description: Additional file 1. Link to the GitHub repository containing code for replicating analysis.
DOI: 10.6084/m9.figshare.14168584
title: Additional file 1 of Six months in: pandemic crime trends in England and Wales

description: Additional file 1. Link to the GitHub repository containing code for replicating analysis.
DOI: 10.6084/m9.figshare.14538981.v1
title: Additional file 2 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 2: Table S1. Differential ATAC peak regions.
DOI: 10.6084/m9.figshare.14538987
title: Additional file 4 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 4: Table S3. ChIP-seq annotated peak regions.
DOI: 10.6084/m9.figshare.14538987.v1
title: Additional file 4 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 4: Table S3. ChIP-seq annotated peak regions.
DOI: 10.6084/m9.figshare.14538984.v1
title: Additional file 3 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 3: Table S2. ChIP-seq differential binding sites.
DOI: 10.6084/m9.figshare.14538993
title: Additional file 6 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 6: Table S5. ATAC-seq and RNA-seq correlation.
DOI: 10.6084/m9.figshare.14538981
title: Additional file 2 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 2: Table S1. Differential ATAC peak regions.
DOI: 10.6084/m9.figshare.14538984
title: Additional file 3 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 3: Table S2. ChIP-seq differential binding sites.
DOI: 10.6084/m9.figshare.14538990
title: Additional file 5 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 5: Table S4. RNA-seq differentially expressed genes.
DOI: 10.6084/m9.figshare.14538996
title: Additional file 7 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 7: Table S6. Ortholog pairs.
DOI: 10.6084/m9.figshare.14538996.v1
title: Additional file 7 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 7: Table S6. Ortholog pairs.
DOI: 10.6084/m9.figshare.14538990.v1
title: Additional file 5 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 5: Table S4. RNA-seq differentially expressed genes.
DOI: 10.6084/m9.figshare.14538999
title: Additional file 8 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 8: Table S7. Orthologous gene list.
DOI: 10.6084/m9.figshare.14538999.v1
title: Additional file 8 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 8: Table S7. Orthologous gene list.
DOI: 10.6084/m9.figshare.14539002
title: Additional file 9 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 9: Table S8. Sequencing QC summary.
DOI: 10.6084/m9.figshare.14539002.v1
title: Additional file 9 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 9: Table S8. Sequencing QC summary.
DOI: 10.6084/m9.figshare.14538993.v1
title: Additional file 6 of Role of epigenetics in unicellular to multicellular transition in Dictyostelium

description: Additional file 6: Table S5. ATAC-seq and RNA-seq correlation.
DOI: 10.6084/m9.figshare.14539014
title: Additional file 10 of Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

description: Additional file 10: Table S9. List of SNPs mapping to 370 porcine miRNA loci and segregating in the 5 Duroc boars that sired the Lipgen population (N = 345).
DOI: 10.6084/m9.figshare.14539014.v1
title: Additional file 10 of Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

description: Additional file 10: Table S9. List of SNPs mapping to 370 porcine miRNA loci and segregating in the 5 Duroc boars that sired the Lipgen population (N = 345).
DOI: 10.6084/m9.figshare.14539017
title: Additional file 11 of Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

description: Additional file 11: Table S10. Association analyses between SNPs in miRNA genes and the mRNA levels of their predicted targets in the gluteus medius (GM) skeletal muscle and liver tissues of Lipgen pigs.
DOI: 10.6084/m9.figshare.14539017.v1
title: Additional file 11 of Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

description: Additional file 11: Table S10. Association analyses between SNPs in miRNA genes and the mRNA levels of their predicted targets in the gluteus medius (GM) skeletal muscle and liver tissues of Lipgen pigs.
DOI: 10.6084/m9.figshare.14539020.v1
title: Additional file 12 of Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes

description: Additional file 12: Table S11. Genomic coordinates and sequence of the seed (miRNA) and its predicted 3′UTR binding site (mRNA) for putative miRNA–mRNA pairs showing significant associations after multiple testing correction (q-value