cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17608/k6.auckland.16689538
title: Supplementary Methods and Tables of Machine learning identifies six genetic variants and alterations in the Heart Atrial Appendage as key contributors to PD risk predictivity

description: Supplementary Methods and Tables of Machine learning identifies six genetic variants and alterations in the Heart Atrial Appendage as key contributors to PD risk predictivity.
DOI: 10.6084/m9.figshare.16689645
title: Additional file 1 of The Nereid on the rise: Platynereis as a model system

description: Additional file 1: Table S1. List of techniques.
DOI: 10.6084/m9.figshare.16689645.v1
title: Additional file 1 of The Nereid on the rise: Platynereis as a model system

description: Additional file 1: Table S1. List of techniques.
DOI: 10.6084/m9.figshare.16689648
title: Additional file 2 of The Nereid on the rise: Platynereis as a model system

description: Additional file 2: Table S2. List of available wild-type and mutant strains.
DOI: 10.6084/m9.figshare.16689648.v1
title: Additional file 2 of The Nereid on the rise: Platynereis as a model system

description: Additional file 2: Table S2. List of available wild-type and mutant strains.
DOI: 10.6084/m9.figshare.14594135
title: Additional file 1 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 1: Table S1. Sample metadata. Detailed metadata, raw read count, and the percent of reads that map to green (Chelonia mydas) turtle hemoglobin genes for each individual (n = 43) included in this study. Individuals without straight carapace length (SCL) denoted were not measured for these parameters.
DOI: 10.6084/m9.figshare.14594138
title: Additional file 2 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 2: Table S2. Annotation and orthogroup information for green turtle blood transcriptome assembly transcripts. Transcripts that did not match to a Gene Ontology (GO) ID are not included.
DOI: 10.6084/m9.figshare.14594135.v1
title: Additional file 1 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 1: Table S1. Sample metadata. Detailed metadata, raw read count, and the percent of reads that map to green (Chelonia mydas) turtle hemoglobin genes for each individual (n = 43) included in this study. Individuals without straight carapace length (SCL) denoted were not measured for these parameters.
DOI: 10.6084/m9.figshare.14594138.v1
title: Additional file 2 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 2: Table S2. Annotation and orthogroup information for green turtle blood transcriptome assembly transcripts. Transcripts that did not match to a Gene Ontology (GO) ID are not included.
DOI: 10.6084/m9.figshare.14594141
title: Additional file 3 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 3: Table S3. KEGG pathway analyses results. KEGG pathways for the green turtle transcriptome and the leatherback multi-tissue assembly.
DOI: 10.6084/m9.figshare.14594141.v1
title: Additional file 3 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 3: Table S3. KEGG pathway analyses results. KEGG pathways for the green turtle transcriptome and the leatherback multi-tissue assembly.
DOI: 10.6084/m9.figshare.14594144
title: Additional file 4 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 4: Table S4. Annotation and orthogroup information for leatherback multi-tissue transcriptome assembly transcripts. Transcripts that did not match to a Gene Ontology (GO) ID are not included.
DOI: 10.6084/m9.figshare.14594150.v1
title: Additional file 6 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 6: Table S6. Tissue-specific orthogroups. Orthogroups and the transcripts that belong to each orthogroup from each individual tissue-type leatherback transcriptome.
DOI: 10.6084/m9.figshare.14594153
title: Additional file 7 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 7: Table S7. Differential orthogroup expression analyses results for comparisons between marine turtle species. Log fold change and adjusted p-values are listed for the green v. leatherback, green v. hawksbill, and leatherback v. hawksbill turtle comparisons.
DOI: 10.6084/m9.figshare.14594144.v1
title: Additional file 4 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 4: Table S4. Annotation and orthogroup information for leatherback multi-tissue transcriptome assembly transcripts. Transcripts that did not match to a Gene Ontology (GO) ID are not included.
DOI: 10.6084/m9.figshare.14594156
title: Additional file 8 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 8: Table S8. Differential gene expression analyses results for comparisons between green turtle foraging aggregations. Log fold change and adjusted p-values are listed for the California and Hawai’i, California and the Commonwealth of the Northern Mariana Islands (CNMI), and Hawai’i and CNMI Islands comparisons.
DOI: 10.6084/m9.figshare.14594147
title: Additional file 5 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 5: Table S5. Species-specific orthogroups. Orthogroups and the transcripts that belong to each orthogroup from each species-specific blood transcriptome.
DOI: 10.6084/m9.figshare.14594147.v1
title: Additional file 5 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 5: Table S5. Species-specific orthogroups. Orthogroups and the transcripts that belong to each orthogroup from each species-specific blood transcriptome.
DOI: 10.6084/m9.figshare.14594150
title: Additional file 6 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 6: Table S6. Tissue-specific orthogroups. Orthogroups and the transcripts that belong to each orthogroup from each individual tissue-type leatherback transcriptome.
DOI: 10.6084/m9.figshare.14594159
title: Additional file 9 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 9: Table S9. Functional enrichment analysis results. Functional enrichment analysis results for contrasts between green turtle foraging aggregations.
DOI: 10.6084/m9.figshare.14594153.v1
title: Additional file 7 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 7: Table S7. Differential orthogroup expression analyses results for comparisons between marine turtle species. Log fold change and adjusted p-values are listed for the green v. leatherback, green v. hawksbill, and leatherback v. hawksbill turtle comparisons.
DOI: 10.6084/m9.figshare.14594156.v1
title: Additional file 8 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 8: Table S8. Differential gene expression analyses results for comparisons between green turtle foraging aggregations. Log fold change and adjusted p-values are listed for the California and Hawai’i, California and the Commonwealth of the Northern Mariana Islands (CNMI), and Hawai’i and CNMI Islands comparisons.
DOI: 10.6084/m9.figshare.14594159.v1
title: Additional file 9 of Species and population specific gene expression in blood transcriptomes of marine turtles

description: Additional file 9: Table S9. Functional enrichment analysis results. Functional enrichment analysis results for contrasts between green turtle foraging aggregations.
DOI: 10.6084/m9.figshare.16530221
title: Additional file 1 of Three different mutations in the DNA topoisomerase 1B in Leishmania infantum contribute to resistance to antitumor drug topotecan

description: Additional file 1: Dataset S1. Log2-transformed 16 × TPT-resistant mutants/WT reads ratios for non-overlapping 5 kb genomic windows for the 36 L. infantum chromosomes in the three TPT-resistant strains.
DOI: 10.6084/m9.figshare.16530221.v1
title: Additional file 1 of Three different mutations in the DNA topoisomerase 1B in Leishmania infantum contribute to resistance to antitumor drug topotecan

description: Additional file 1: Dataset S1. Log2-transformed 16 × TPT-resistant mutants/WT reads ratios for non-overlapping 5 kb genomic windows for the 36 L. infantum chromosomes in the three TPT-resistant strains.
DOI: 10.6084/m9.figshare.16530224.v1
title: Additional file 2 of Three different mutations in the DNA topoisomerase 1B in Leishmania infantum contribute to resistance to antitumor drug topotecan

description: Additional file 2: Dataset S2. Homozygous and heterozygous SNPs in the different TPT-resistant mutants.
DOI: 10.6084/m9.figshare.16530224
title: Additional file 2 of Three different mutations in the DNA topoisomerase 1B in Leishmania infantum contribute to resistance to antitumor drug topotecan

description: Additional file 2: Dataset S2. Homozygous and heterozygous SNPs in the different TPT-resistant mutants.
DOI: 10.6084/m9.figshare.16689669
title: Additional file 10 of Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

description: Additional file 10 S10 File. .xlsx file containing tables of gene set enrichment results, including annotated gene set clusters.
DOI: 10.6084/m9.figshare.16689669.v1
title: Additional file 10 of Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

description: Additional file 10 S10 File. .xlsx file containing tables of gene set enrichment results, including annotated gene set clusters.
DOI: 10.6084/m9.figshare.16689672
title: Additional file 11 of Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

description: Additional file 11 S11 File. .xlsx file containing tables of gene lists for all differential expression contrasts using batch 3 samples only.
DOI: 10.6084/m9.figshare.16689672.v1
title: Additional file 11 of Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

description: Additional file 11 S11 File. .xlsx file containing tables of gene lists for all differential expression contrasts using batch 3 samples only.
DOI: 10.6084/m9.figshare.16689702.v1
title: Additional file 8 of Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

description: Additional file 8 S8 File. .xlsx file containing tables of gene lists for all differential expression contrasts.
DOI: 10.6084/m9.figshare.16689702
title: Additional file 8 of Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

description: Additional file 8 S8 File. .xlsx file containing tables of gene lists for all differential expression contrasts.
DOI: 10.6084/m9.figshare.16689705
title: Additional file 9 of Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

description: Additional file 9 S9 File. .xlsx file containing tables of significantly over- and underrepresented biological processes for up- and downregulated genes for each differential expression contrast.
DOI: 10.6084/m9.figshare.16689705.v1
title: Additional file 9 of Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

description: Additional file 9 S9 File. .xlsx file containing tables of significantly over- and underrepresented biological processes for up- and downregulated genes for each differential expression contrast.
DOI: 10.6084/m9.figshare.16689713
title: Additional file 3 of Studying dietary intake in daily life through multilevel two-part modelling: a novel analytical approach and its practical application

description: Additional file 3. R Code.
DOI: 10.6084/m9.figshare.16689710
title: Additional file 2 of Studying dietary intake in daily life through multilevel two-part modelling: a novel analytical approach and its practical application

description: Additional file 2. Dataset.
DOI: 10.6084/m9.figshare.16689710.v1
title: Additional file 2 of Studying dietary intake in daily life through multilevel two-part modelling: a novel analytical approach and its practical application

description: Additional file 2. Dataset.
DOI: 10.6084/m9.figshare.16689713.v1
title: Additional file 3 of Studying dietary intake in daily life through multilevel two-part modelling: a novel analytical approach and its practical application

description: Additional file 3. R Code.
DOI: 10.6084/m9.figshare.16689839
title: Additional file 1 of Female developmental environment delays development of male honeybee (Apis mellifera)

description: Additional file 1: Supplementary figures. This file has included a set of 3 supplementary figures providing: Pearson’s correlation coefficient analysis of 18 samples (Figure S1); Expression of 10 genes in three comparisons at 3rd instar stage by qRT-PCR (Figure S2); Expression of 10 genes in three comparisons at newly emerged stage by qRT-PCR (Figure S3).
DOI: 10.6084/m9.figshare.16689839.v1
title: Additional file 1 of Female developmental environment delays development of male honeybee (Apis mellifera)

description: Additional file 1: Supplementary figures. This file has included a set of 3 supplementary figures providing: Pearson’s correlation coefficient analysis of 18 samples (Figure S1); Expression of 10 genes in three comparisons at 3rd instar stage by qRT-PCR (Figure S2); Expression of 10 genes in three comparisons at newly emerged stage by qRT-PCR (Figure S3).
DOI: 10.6084/m9.figshare.16689842.v1
title: Additional file 2 of Female developmental environment delays development of male honeybee (Apis mellifera)

description: Additional file 2: Supplementary tables. This file has included a set of 12 supplementary figures providing: Statistics of sequencing data (Table S1); Statistical table of sample sequencing data and sequence alignment of selected reference genomes (Table S2); DEGs between QC and DC larvae (Table S3); DEGs between WC and DC larvae (Table S4); DEGs between QC and DC drones (Table S5); DEGs between WC and DC drones (Table S6); DEGs between QC and DC larvae enriched in GO enrichment (Table S7) DEGs between WC and DC larvae enriched in GO enrichment (Table S8); DEGs between QC and DC drones enriched in GO enrichment (Table S9); DEGs between WC and DC drones enriched in GO enrichment (Table S10); DEGs between drones from male cells and female cells enriched in 17 important KEGG pathways (Table S11, the data is the raw data supporting the Fig. 6); qRT-PCR primer sequences (Table S12).
DOI: 10.6084/m9.figshare.16689842
title: Additional file 2 of Female developmental environment delays development of male honeybee (Apis mellifera)

description: Additional file 2: Supplementary tables. This file has included a set of 12 supplementary figures providing: Statistics of sequencing data (Table S1); Statistical table of sample sequencing data and sequence alignment of selected reference genomes (Table S2); DEGs between QC and DC larvae (Table S3); DEGs between WC and DC larvae (Table S4); DEGs between QC and DC drones (Table S5); DEGs between WC and DC drones (Table S6); DEGs between QC and DC larvae enriched in GO enrichment (Table S7) DEGs between WC and DC larvae enriched in GO enrichment (Table S8); DEGs between QC and DC drones enriched in GO enrichment (Table S9); DEGs between WC and DC drones enriched in GO enrichment (Table S10); DEGs between drones from male cells and female cells enriched in 17 important KEGG pathways (Table S11, the data is the raw data supporting the Fig. 6); qRT-PCR primer sequences (Table S12).
DOI: 10.6084/m9.figshare.16689798
title: Additional file 12 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 12: Table S1. Total number of ones, zeros and nulls in the sparse matrix for the 163 TFs used in this study.
DOI: 10.6084/m9.figshare.16689798.v1
title: Additional file 12 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 12: Table S1. Total number of ones, zeros and nulls in the sparse matrix for the 163 TFs used in this study.
DOI: 10.6084/m9.figshare.16689801.v1
title: Additional file 13 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 13: Table S2. Performance for 148 TFs on the original multi-model of 50 TFs, as well as on individual models trained with and without transfer learning. An empty value for multi-model performance indicates that the TF was not used to train the multi-model.
DOI: 10.6084/m9.figshare.16689801
title: Additional file 13 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 13: Table S2. Performance for 148 TFs on the original multi-model of 50 TFs, as well as on individual models trained with and without transfer learning. An empty value for multi-model performance indicates that the TF was not used to train the multi-model.
DOI: 10.6084/m9.figshare.16689804
title: Additional file 14 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 14: Table S3. List of TF binding modes used in this study.
DOI: 10.6084/m9.figshare.16689804.v1
title: Additional file 14 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 14: Table S3. List of TF binding modes used in this study.
DOI: 10.6084/m9.figshare.16689807
title: Additional file 15 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 15: Table S4. Tomtom similarities of TF profiles from the JASPAR database to the first convolutional layer filters of the original multi-model of 50 TFs, the individual models of HNF4A and SP1, trained with and without transfer learning, and the individual models of JUND trained with transfer learning from multi-models pre-trained on either five cofactors or five random TFs as well as trained from scratch.
DOI: 10.6084/m9.figshare.16689807.v1
title: Additional file 15 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 15: Table S4. Tomtom similarities of TF profiles from the JASPAR database to the first convolutional layer filters of the original multi-model of 50 TFs, the individual models of HNF4A and SP1, trained with and without transfer learning, and the individual models of JUND trained with transfer learning from multi-models pre-trained on either five cofactors or five random TFs as well as trained from scratch.
DOI: 10.6084/m9.figshare.16689813
title: Additional file 16 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 16: Table S5. Transfer learning performance for 148 TFs with and without freezing of the convolutional layers.
DOI: 10.6084/m9.figshare.16689813.v1
title: Additional file 16 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 16: Table S5. Transfer learning performance for 148 TFs with and without freezing of the convolutional layers.
DOI: 10.6084/m9.figshare.16689816.v1
title: Additional file 17 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 17: Table S6. List of 50 non-redudant JASPAR profiles used to initialize convolutional filter weights.
DOI: 10.6084/m9.figshare.16689816
title: Additional file 17 of Biologically relevant transfer learning improves transcription factor binding prediction

description: Additional file 17: Table S6. List of 50 non-redudant JASPAR profiles used to initialize convolutional filter weights.
DOI: 10.6084/m9.figshare.16689861
title: Additional file 10 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 10. Differentially expressed gene analysis comparing CD44low and CD44high samples derived from lung tissue.
DOI: 10.6084/m9.figshare.16689861.v1
title: Additional file 10 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 10. Differentially expressed gene analysis comparing CD44low and CD44high samples derived from lung tissue.
DOI: 10.6084/m9.figshare.16689864
title: Additional file 11 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 11. Differentially expressed gene analysis comparing CD44low and CD44high samples derived from lymph node tissue.
DOI: 10.6084/m9.figshare.16689864.v1
title: Additional file 11 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 11. Differentially expressed gene analysis comparing CD44low and CD44high samples derived from lymph node tissue.
DOI: 10.6084/m9.figshare.16689867.v1
title: Additional file 12 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 12. Complete list of enriched GO-terms and upregulated genes for CD44high samples across all tissues (from Fig 3A).
DOI: 10.6084/m9.figshare.16689867
title: Additional file 12 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 12. Complete list of enriched GO-terms and upregulated genes for CD44high samples across all tissues (from Fig 3A).
DOI: 10.6084/m9.figshare.16689870
title: Additional file 13 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 13. Complete list of enriched GO-terms and upregulated genes for CD44low samples across all tissues (from Fig 3A).
DOI: 10.6084/m9.figshare.16689873
title: Additional file 14 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 14. Complete list of enriched GO-terms and upregulated genes from CD44high vs. CD44low lymph node-derived samples (Fig 3B).
DOI: 10.6084/m9.figshare.16689870.v1
title: Additional file 13 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 13. Complete list of enriched GO-terms and upregulated genes for CD44low samples across all tissues (from Fig 3A).
DOI: 10.6084/m9.figshare.16689873.v1
title: Additional file 14 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 14. Complete list of enriched GO-terms and upregulated genes from CD44high vs. CD44low lymph node-derived samples (Fig 3B).
DOI: 10.6084/m9.figshare.16689876
title: Additional file 15 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 15. Complete list of enriched GO-terms and upregulated genes from CD44low vs. CD44high lymph node-derived samples (Fig 3B).
DOI: 10.6084/m9.figshare.16689876.v1
title: Additional file 15 of Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

description: Additional file 15. Complete list of enriched GO-terms and upregulated genes from CD44low vs. CD44high lymph node-derived samples (Fig 3B).