cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12422363
title: Additional file 2 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 2: Table S1. Result of mt-gRNA specificity prediction. Table S2. Result of cp-gRNA specificity prediction.
DOI: 10.6084/m9.figshare.12422372
title: Additional file 3 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 3: Table S3. Summary of soil 799F-1193R amplicon data. Table S4. Differential OTUs in soil samples (Cas-16S-seq vs regular 16S-seq).
DOI: 10.6084/m9.figshare.12422363.v1
title: Additional file 2 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 2: Table S1. Result of mt-gRNA specificity prediction. Table S2. Result of cp-gRNA specificity prediction.
DOI: 10.6084/m9.figshare.12422372.v1
title: Additional file 3 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 3: Table S3. Summary of soil 799F-1193R amplicon data. Table S4. Differential OTUs in soil samples (Cas-16S-seq vs regular 16S-seq).
DOI: 10.6084/m9.figshare.12422378.v1
title: Additional file 4 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 4: Table S5. Summary of root 799F-1193R amplicon data. Table S6. Differential OTUs in root samples (Cas-16S-seq vs regular 16S-seq).
DOI: 10.6084/m9.figshare.12422387.v1
title: Additional file 6 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 6: Table S9. Primers used for in vitro transcription of gRNA. Table S10. Primer oligos used for 16S rRNA gene amplification.
DOI: 10.6084/m9.figshare.12422384
title: Additional file 5 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 5: Table S7. Summary of 515F-806R amplicon result. Table S8. Abundance of bacterial OTUs detected in leaf 515F-806R amplicons.
DOI: 10.6084/m9.figshare.12422378
title: Additional file 4 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 4: Table S5. Summary of root 799F-1193R amplicon data. Table S6. Differential OTUs in root samples (Cas-16S-seq vs regular 16S-seq).
DOI: 10.6084/m9.figshare.12422387
title: Additional file 6 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 6: Table S9. Primers used for in vitro transcription of gRNA. Table S10. Primer oligos used for 16S rRNA gene amplification.
DOI: 10.6084/m9.figshare.11954097
title: Additional file 5 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 5: Supplementary Table SII. Relative quantification of S. flexneri and S. bongori results for the 27 S. flexneri/S. bongori samples.
DOI: 10.6084/m9.figshare.12422384.v1
title: Additional file 5 of Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing

description: Additional file 5: Table S7. Summary of 515F-806R amplicon result. Table S8. Abundance of bacterial OTUs detected in leaf 515F-806R amplicons.
DOI: 10.6084/m9.figshare.11954106.v1
title: Additional file 6 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 6: Supplementary Table SIII. Proteins identified and SC quantified in the 27 S. flexneri/S. bongori samples.
DOI: 10.6084/m9.figshare.11954088
title: Additional file 4 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 4: Supplementary Table SI. Proteomic results for the 27 S. flexneri/S. bongori samples.
DOI: 10.6084/m9.figshare.13237427
title: Compering long MLEs sequences with 500bp flank site

description: The nucleotide sequences data of the Acc_MLE_10 plus flanking 500bp and long MLEs encoding complete transposase plus flanking 500bp in Am, Ack, Acj, Ad, Af, and results of compering of the Acc sequences with the other sequnces.<b></b>
DOI: 10.6084/m9.figshare.11954112
title: Additional file 7 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 7: Supplementary Table SIV. Quantitation of a mock community sample with same protein content per organism from Kleiner et al.
DOI: 10.6084/m9.figshare.11954097.v1
title: Additional file 5 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 5: Supplementary Table SII. Relative quantification of S. flexneri and S. bongori results for the 27 S. flexneri/S. bongori samples.
DOI: 10.6084/m9.figshare.11954112.v1
title: Additional file 7 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 7: Supplementary Table SIV. Quantitation of a mock community sample with same protein content per organism from Kleiner et al.
DOI: 10.6084/m9.figshare.11954106
title: Additional file 6 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 6: Supplementary Table SIII. Proteins identified and SC quantified in the 27 S. flexneri/S. bongori samples.
DOI: 10.6084/m9.figshare.11954088.v1
title: Additional file 4 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 4: Supplementary Table SI. Proteomic results for the 27 S. flexneri/S. bongori samples.
DOI: 10.6084/m9.figshare.13237427.v1
title: Compering long MLEs sequences with 500bp flank site

description: The nucleotide sequences data of the Acc_MLE_10 plus flanking 500bp and long MLEs encoding complete transposase plus flanking 500bp in Am, Ack, Acj, Ad, Af, and results of compering of the Acc sequences with the other sequnces.<b></b>
DOI: 10.6084/m9.figshare.13237765
title: Additional file 1 of S&P BSE Sensex and S&P BSE IT return forecasting using ARIMA

description: Additional file 1.
DOI: 10.6084/m9.figshare.13237765.v1
title: Additional file 1 of S&P BSE Sensex and S&P BSE IT return forecasting using ARIMA

description: Additional file 1.
DOI: 10.6084/m9.figshare.13237795
title: Additional file 6 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 6: Table S1. Top 20 genes for each cluster from full human choroidal sc-RNA-seq data set. Excel file of gene names, cluster, adjusted p-value (p_val_adj), percent of cells expressing gene (pct.1 = current cluster, pct.2 = all other clusters), fold change (avg_logFC = natural log fold change), and raw p-value (p_val).
DOI: 10.6084/m9.figshare.13237798.v1
title: Additional file 7 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 7: Table S2. Top 25 genes for each cluster of the leukocytes from human choroidal sc-RNA-seq data set. Excel file of gene names, cluster, adjusted p-value (p_val_adj), percent of cells expressing gene (pct.1 = current cluster, pct.2 = all other clusters), fold change (avg_logFC = natural log fold change), and raw p-value (p_val).
DOI: 10.6084/m9.figshare.13237777
title: Additional file 10 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 10: Table S4. GO and REVIGO outputs for up- and down-regulated genes from each macrophage subtype. For GO tabs: Excel file of GO terms, description of GO term, p-value, FDR q-value, fold enrichment, number of genes expressed in macrophages (N), number of genes in GO term (B), number of differentially expressed genes (n), number of differentially expressed genes in the GO term (b), and the specific genes that were differentially expressed in the GO term. For REVIGO tabs: Excel file of GO term (term_ID), description of GO term, frequency, plotting information, log10 p-value, uniqueness, dispensability, and whether or not the term was eliminated (0 = no, 1 = yes) due to dispensability.
DOI: 10.6084/m9.figshare.13237804.v1
title: Additional file 9 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 9: Table S4. List of differentially expressed genes between macrophage subtypes. Excel file of gene names, cluster, adjusted p-value (p_val_adj), percent of cells expressing gene (pct.1 = current cluster, pct.2 = all other clusters), fold change (avg_logFC = natural log fold change), and raw p-value (p_val).
DOI: 10.6084/m9.figshare.13237777.v1
title: Additional file 10 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 10: Table S4. GO and REVIGO outputs for up- and down-regulated genes from each macrophage subtype. For GO tabs: Excel file of GO terms, description of GO term, p-value, FDR q-value, fold enrichment, number of genes expressed in macrophages (N), number of genes in GO term (B), number of differentially expressed genes (n), number of differentially expressed genes in the GO term (b), and the specific genes that were differentially expressed in the GO term. For REVIGO tabs: Excel file of GO term (term_ID), description of GO term, frequency, plotting information, log10 p-value, uniqueness, dispensability, and whether or not the term was eliminated (0 = no, 1 = yes) due to dispensability.
DOI: 10.6084/m9.figshare.13237801.v1
title: Additional file 8 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 8: Table S3. Number and percentage of cells from each patient that contributed to each leukocyte cluster. Number of cells, ratio of cells, phenotype of patient, and enrichment of sample from each human donor.
DOI: 10.6084/m9.figshare.13237798
title: Additional file 7 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 7: Table S2. Top 25 genes for each cluster of the leukocytes from human choroidal sc-RNA-seq data set. Excel file of gene names, cluster, adjusted p-value (p_val_adj), percent of cells expressing gene (pct.1 = current cluster, pct.2 = all other clusters), fold change (avg_logFC = natural log fold change), and raw p-value (p_val).
DOI: 10.6084/m9.figshare.13237801
title: Additional file 8 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 8: Table S3. Number and percentage of cells from each patient that contributed to each leukocyte cluster. Number of cells, ratio of cells, phenotype of patient, and enrichment of sample from each human donor.
DOI: 10.6084/m9.figshare.13237795.v1
title: Additional file 6 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 6: Table S1. Top 20 genes for each cluster from full human choroidal sc-RNA-seq data set. Excel file of gene names, cluster, adjusted p-value (p_val_adj), percent of cells expressing gene (pct.1 = current cluster, pct.2 = all other clusters), fold change (avg_logFC = natural log fold change), and raw p-value (p_val).
DOI: 10.6084/m9.figshare.13237804
title: Additional file 9 of Ocular macrophage origin and heterogeneity during steady state and experimental choroidal neovascularization

description: Additional file 9: Table S4. List of differentially expressed genes between macrophage subtypes. Excel file of gene names, cluster, adjusted p-value (p_val_adj), percent of cells expressing gene (pct.1 = current cluster, pct.2 = all other clusters), fold change (avg_logFC = natural log fold change), and raw p-value (p_val).
DOI: 10.6084/m9.figshare.13237818.v1
title: Additional file 3 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 3: Table S2. The Migrate analysis results (using microsatellite data) estimating effective population size of the seven mtDNA clades (Θ1-Θ7). Population 1 represents Ptt-B, population 2 represents Pv-B, population 3 represents Ptr, population 4 represents Ptt-C, population 5 represents Ptt-A, population 6 represents Pv-A, and population 7 represents Ptt-D. In terms of potential gene flow rate (M), M1-&gt;2 denotes the gene flow rate from Ptt-B to Pv-B. The directional gene flow occurring in the two intergradation zones, between Ptt-B and Pv-B, and between Pv-B and Ptt-C is in bold.
DOI: 10.6084/m9.figshare.13237818
title: Additional file 3 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 3: Table S2. The Migrate analysis results (using microsatellite data) estimating effective population size of the seven mtDNA clades (Θ1-Θ7). Population 1 represents Ptt-B, population 2 represents Pv-B, population 3 represents Ptr, population 4 represents Ptt-C, population 5 represents Ptt-A, population 6 represents Pv-A, and population 7 represents Ptt-D. In terms of potential gene flow rate (M), M1-&gt;2 denotes the gene flow rate from Ptt-B to Pv-B. The directional gene flow occurring in the two intergradation zones, between Ptt-B and Pv-B, and between Pv-B and Ptt-C is in bold.
DOI: 10.6084/m9.figshare.13237830
title: Additional file 7 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 7: Table S14. Allele size ranges, repeat motifs with their NCBI GenBank accession numbers, multiple-mix reaction grouping schemes, the oligo-nucleotide sequences of primers with dyes, optimal annealing temperatures and the sources of primers of all microsatellite DNA markers tested in this study. "NA" indicates the primer pair failed to amplify.
DOI: 10.6084/m9.figshare.13237809.v1
title: Additional file 10 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 10: Table S19. The correlation matrix retrieved from the correlation test between each pair of bioclimatic variables. The R-square values varied from zero to one, with "zero" representing no correlation and "one" representing 100% correlation. The bioclimatic variables (in bold) are the ones used in further niche modelling analyses after trimming variables showing strong correlation. The pairwise values (R-square) &gt; 70 or &lt; -70 were considered as strong correlations. All pairwise R-square values showing a strong correlation between bioclimatic variables are underlined.
DOI: 10.6084/m9.figshare.13237824
title: Additional file 5 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 5: Table S11. List of all samples, their corresponding localities and NCBI GenBank accession numbers across different genes. All NCBI accessions of outgroups used in this study are given at the bottom.
DOI: 10.6084/m9.figshare.13237827
title: Additional file 6 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 6: Table S12. List of primers used in the study with corresponding oligo sequences, optimized annealing temperatures and sources.
DOI: 10.6084/m9.figshare.13237815
title: Additional file 2 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 2: Table S1. The sequence polymorphisms of all genes used in this study, including fragment length (bp), number of variable sites, variable site percentage, parsimony informative sites, and the percentage of parsimony informative sites.
DOI: 10.6084/m9.figshare.13237815.v1
title: Additional file 2 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 2: Table S1. The sequence polymorphisms of all genes used in this study, including fragment length (bp), number of variable sites, variable site percentage, parsimony informative sites, and the percentage of parsimony informative sites.
DOI: 10.6084/m9.figshare.13237824.v1
title: Additional file 5 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 5: Table S11. List of all samples, their corresponding localities and NCBI GenBank accession numbers across different genes. All NCBI accessions of outgroups used in this study are given at the bottom.
DOI: 10.6084/m9.figshare.13237833.v1
title: Additional file 8 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 8: Table S15. The genotyping results of 14 microsatellite DNA loci used in this study, together with locality and subpopulation information.
DOI: 10.6084/m9.figshare.13237836
title: Additional file 9 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 9: Table S18. The bioclimatic variables and their percentage contribution, permutation importance and jack-knife test AUC’s used in the ENM to determine suitable habitat ranges of the P. tentorius species complex. Variables with AUC above 0.75 were considered as potentially useful (given in bold).
DOI: 10.6084/m9.figshare.13237833
title: Additional file 8 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 8: Table S15. The genotyping results of 14 microsatellite DNA loci used in this study, together with locality and subpopulation information.
DOI: 10.6084/m9.figshare.13237821
title: Additional file 4 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 4: Table S10. The climatic variables that made significant impacts in each group across different periods (group abbreviations as in Table S6) from the ENM analyses.
DOI: 10.6084/m9.figshare.13237821.v1
title: Additional file 4 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 4: Table S10. The climatic variables that made significant impacts in each group across different periods (group abbreviations as in Table S6) from the ENM analyses.
DOI: 10.6084/m9.figshare.13237830.v1
title: Additional file 7 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 7: Table S14. Allele size ranges, repeat motifs with their NCBI GenBank accession numbers, multiple-mix reaction grouping schemes, the oligo-nucleotide sequences of primers with dyes, optimal annealing temperatures and the sources of primers of all microsatellite DNA markers tested in this study. "NA" indicates the primer pair failed to amplify.
DOI: 10.6084/m9.figshare.13237827.v1
title: Additional file 6 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 6: Table S12. List of primers used in the study with corresponding oligo sequences, optimized annealing temperatures and sources.
DOI: 10.6084/m9.figshare.13237836.v1
title: Additional file 9 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 9: Table S18. The bioclimatic variables and their percentage contribution, permutation importance and jack-knife test AUC’s used in the ENM to determine suitable habitat ranges of the P. tentorius species complex. Variables with AUC above 0.75 were considered as potentially useful (given in bold).
DOI: 10.6084/m9.figshare.13237809
title: Additional file 10 of Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

description: Additional file 10: Table S19. The correlation matrix retrieved from the correlation test between each pair of bioclimatic variables. The R-square values varied from zero to one, with "zero" representing no correlation and "one" representing 100% correlation. The bioclimatic variables (in bold) are the ones used in further niche modelling analyses after trimming variables showing strong correlation. The pairwise values (R-square) &gt; 70 or &lt; -70 were considered as strong correlations. All pairwise R-square values showing a strong correlation between bioclimatic variables are underlined.