cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25919/5f45ca3203f62
title: CSIRO Film Collection: videos 201 - 299 - archival versions

description: CSIRO produced its first film in 1946. It was a two-hour, five-part epic in black and white designed for a specialist audience of Commonwealth scientists meeting in London. It showed them - in the most graphic way possible at the time - the nature and extent of the research facilities of an organisation embarking on the problems of post-war reconstruction. Within a few years, a permanent film unit was established and began to specialise in producing films for the specific audiences on particular areas of research. By the 1960's, it became apparent that many of the films were of interest to a much wider audience. Schools, colleges and universities were beginning to introduce the audio-visual medium to the learning process and CSIRO films were in increasing demand. Makers of television programmes looked to CSIRO films for images of science not yet accessible to the public eye.
DOI: 10.6084/m9.figshare.8222258
title: MOESM3 of Molecular profiling of microinvasive breast cancer microenvironment progression

description: Additional file 3. List of genes observed in the stromal portions involved in the metabolism. The fold change values comparing S-NBE versus S-EIF and S-NBE versus S-IBC are reported.
DOI: 10.6084/m9.figshare.8222258.v1
title: MOESM3 of Molecular profiling of microinvasive breast cancer microenvironment progression

description: Additional file 3. List of genes observed in the stromal portions involved in the metabolism. The fold change values comparing S-NBE versus S-EIF and S-NBE versus S-IBC are reported.
DOI: 10.6084/m9.figshare.8222261
title: Additional file 6: of A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

description: Lists of miRNAs detected in all libraries with 5 million raw reads, including number of reads for each miRNA. (XLSX 172 kb)
DOI: 10.6084/m9.figshare.8222249
title: MOESM2 of Molecular profiling of microinvasive breast cancer microenvironment progression

description: Additional file 2. List of observed genes in the epithelial portions involved in the metabolism. The fold change values comparing NBE and tumor portions are reported.
DOI: 10.6084/m9.figshare.8222246
title: Additional file 4: of A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

description: All differentially detected miRNAs. a. Differentially detected miRNAs between library preparations (NEXTflex and QIAseq) in MagnaZol and miRNeasy extractions. Positive fold change indicates a higher detection in QIAseq and negative fold-change indicates higher detection in NEXTflex. b. Differentially detected miRNAs between RNA extractions (MagnaZol and miRNeasy) in NEXTflex and QIAseq library preparations. Positive fold change indicates higher detection in MagnaZol, negative fold change indicates higher detection in miRNeasy. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8222249.v1
title: MOESM2 of Molecular profiling of microinvasive breast cancer microenvironment progression

description: Additional file 2. List of observed genes in the epithelial portions involved in the metabolism. The fold change values comparing NBE and tumor portions are reported.
DOI: 10.6084/m9.figshare.8222261.v1
title: Additional file 6: of A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

description: Lists of miRNAs detected in all libraries with 5 million raw reads, including number of reads for each miRNA. (XLSX 172 kb)
DOI: 10.6084/m9.figshare.8222240
title: MOESM1 of Molecular profiling of microinvasive breast cancer microenvironment progression

description: Additional file 1. Complete list of DEGs derived from all the comparisons: S-NBE versus S-EIF, S-NBE versus S-IBC and S-NBE versus S-EIF.
DOI: 10.6084/m9.figshare.8222246.v1
title: Additional file 4: of A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

description: All differentially detected miRNAs. a. Differentially detected miRNAs between library preparations (NEXTflex and QIAseq) in MagnaZol and miRNeasy extractions. Positive fold change indicates a higher detection in QIAseq and negative fold-change indicates higher detection in NEXTflex. b. Differentially detected miRNAs between RNA extractions (MagnaZol and miRNeasy) in NEXTflex and QIAseq library preparations. Positive fold change indicates higher detection in MagnaZol, negative fold change indicates higher detection in miRNeasy. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8222234
title: Additional file 2: of A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

description: Sequences matching plant miRNAs. (CSV 505 kb)
DOI: 10.6084/m9.figshare.8222240.v1
title: MOESM1 of Molecular profiling of microinvasive breast cancer microenvironment progression

description: Additional file 1. Complete list of DEGs derived from all the comparisons: S-NBE versus S-EIF, S-NBE versus S-IBC and S-NBE versus S-EIF.
DOI: 10.6084/m9.figshare.8222225
title: Additional file 8: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: List of the 60 genes annotated in the 154 FST windows (≥0.3) using INDEL dataset. (XLS 79 kb)
DOI: 10.6084/m9.figshare.8222228
title: Additional file 9: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: Table S1: Genes annotated commonly between selection signatures of two or more datasets. The datasets were the 1941 consensus regions of ROH (cROH), the FST SNP windows (&gt; 0.3), and the FST INDEL windows (&gt; 0.3). (XLS 83 kb)
DOI: 10.6084/m9.figshare.8222225.v1
title: Additional file 8: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: List of the 60 genes annotated in the 154 FST windows (≥0.3) using INDEL dataset. (XLS 79 kb)
DOI: 10.6084/m9.figshare.8222234.v1
title: Additional file 2: of A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

description: Sequences matching plant miRNAs. (CSV 505 kb)
DOI: 10.6084/m9.figshare.8222219
title: Additional file 7: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: List of the 56 genes annotated in the 178 FST windows (≥0.3) using SNP dataset. (XLS 5840 kb)
DOI: 10.6084/m9.figshare.8222219.v1
title: Additional file 7: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: List of the 56 genes annotated in the 178 FST windows (≥0.3) using SNP dataset. (XLS 5840 kb)
DOI: 10.6084/m9.figshare.8222228.v1
title: Additional file 9: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: Table S1: Genes annotated commonly between selection signatures of two or more datasets. The datasets were the 1941 consensus regions of ROH (cROH), the FST SNP windows (&gt; 0.3), and the FST INDEL windows (&gt; 0.3). (XLS 83 kb)
DOI: 10.6084/m9.figshare.8222213
title: Additional file 6: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: List of the 5681 genes annotated in the 1941 consensus regions of runs of homozygosity (cROH). (TXT 2578 kb)
DOI: 10.6084/m9.figshare.8222204
title: Additional file 5: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A text file with information of FST windows using INDEL dataset. Information comprises chromosome (CHR), start (START) and end (END) positions, number of variants (NVAR), and weighted FST values (FST) for each window. (TXT 2830 kb)
DOI: 10.6084/m9.figshare.8222213.v1
title: Additional file 6: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: List of the 5681 genes annotated in the 1941 consensus regions of runs of homozygosity (cROH). (TXT 2578 kb)
DOI: 10.6084/m9.figshare.8222204.v1
title: Additional file 5: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A text file with information of FST windows using INDEL dataset. Information comprises chromosome (CHR), start (START) and end (END) positions, number of variants (NVAR), and weighted FST values (FST) for each window. (TXT 2830 kb)
DOI: 10.6084/m9.figshare.8222198
title: Additional file 4: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A text file with information of FST windows using SNP dataset. Information comprises chromosome (CHR), start (START) and end (END) positions, number of variants (NVAR), and weighted FST values (FST) for each window. (XLSX 19935 kb)
DOI: 10.6084/m9.figshare.8222189
title: Additional file 3: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A text file with information about pools of overlapping ROH among the 28 chickens. Information comprises pool identification (POOL), family identification (FID), individual identification (IID), chromosome (CHR), start (BP1) and end (BP2) positions, size (KB), and number of SNP in each ROH of in the pool. Each pool has n + 2 lines: the n lines are respective to the n individuals in overlap and the last two represents the union and consensus regions of the overlap. (TXT 776 kb)
DOI: 10.6084/m9.figshare.8222198.v1
title: Additional file 4: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A text file with information of FST windows using SNP dataset. Information comprises chromosome (CHR), start (START) and end (END) positions, number of variants (NVAR), and weighted FST values (FST) for each window. (XLSX 19935 kb)
DOI: 10.6084/m9.figshare.8222189.v1
title: Additional file 3: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A text file with information about pools of overlapping ROH among the 28 chickens. Information comprises pool identification (POOL), family identification (FID), individual identification (IID), chromosome (CHR), start (BP1) and end (BP2) positions, size (KB), and number of SNP in each ROH of in the pool. Each pool has n + 2 lines: the n lines are respective to the n individuals in overlap and the last two represents the union and consensus regions of the overlap. (TXT 776 kb)
DOI: 10.6084/m9.figshare.8222180
title: Additional file 9: of Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

description: Table S4. Haplotypes blocks defined by SNPanalyzer 2.0 (XLSX 57 kb)
DOI: 10.6084/m9.figshare.8222183
title: Additional file 1: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A text file with information of the 5721 ROH identified in the analysis with the 28 chickens. Information comprises individual identification (IID), chromosome (CHR), start (POS1) and end (POS2) positions, size (KB), number of SNP in each ROH (NSNP), and density of SNP (DENSITY). (TXT 256 kb)
DOI: 10.6084/m9.figshare.8222186
title: Additional file 2: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A compressed file of images (TIFF format) of genome wide distribution of runs of homozygosity (ROH) in TT population for each chromosome. (RAR 144 kb)
DOI: 10.6084/m9.figshare.8222177
title: Additional file 12: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: positional information of overlaps between cROH of animals of the 7th and 16th generations with ROH of animals of the TT Reference Population. (XLSX 1198 kb)
DOI: 10.6084/m9.figshare.8222186.v1
title: Additional file 2: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A compressed file of images (TIFF format) of genome wide distribution of runs of homozygosity (ROH) in TT population for each chromosome. (RAR 144 kb)
DOI: 10.6084/m9.figshare.8222177.v1
title: Additional file 12: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: positional information of overlaps between cROH of animals of the 7th and 16th generations with ROH of animals of the TT Reference Population. (XLSX 1198 kb)
DOI: 10.6084/m9.figshare.8222180.v1
title: Additional file 9: of Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

description: Table S4. Haplotypes blocks defined by SNPanalyzer 2.0 (XLSX 57 kb)
DOI: 10.6084/m9.figshare.8222183.v1
title: Additional file 1: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: A text file with information of the 5721 ROH identified in the analysis with the 28 chickens. Information comprises individual identification (IID), chromosome (CHR), start (POS1) and end (POS2) positions, size (KB), number of SNP in each ROH (NSNP), and density of SNP (DENSITY). (TXT 256 kb)
DOI: 10.6084/m9.figshare.8222165
title: Additional file 10: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: Table S2: Genes previously associated with traits of interest located in candidate selection signatures. Those located in consensus regions of ROH presents the number of animals sharing the common region, and those located in FST windows present the respective weighted FST values. (XLSX 394 kb)
DOI: 10.6084/m9.figshare.8222168
title: Additional file 7: of Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

description: Table S3. Fst values for SNP loci for Inodurus-related-cantaloupe and Indian pairwise group comparisons (XLSX 283 kb)
DOI: 10.6084/m9.figshare.8222165.v1
title: Additional file 10: of Identification of selection signatures involved in performance traits in a paternal broiler line

description: Table S2: Genes previously associated with traits of interest located in candidate selection signatures. Those located in consensus regions of ROH presents the number of animals sharing the common region, and those located in FST windows present the respective weighted FST values. (XLSX 394 kb)
DOI: 10.6084/m9.figshare.8222168.v1
title: Additional file 7: of Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

description: Table S3. Fst values for SNP loci for Inodurus-related-cantaloupe and Indian pairwise group comparisons (XLSX 283 kb)
DOI: 10.6084/m9.figshare.8222156
title: Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

description: Supplementary Methods: Tasmanian devil reduced-representation sequencing. Table S1. Summary statistics for the resultant SNP loci datasets of three pipelines, filtered less stringently at a higher allowable missing data (30% call rate; cf Table 1), for Tasmanian devil (N = 131) and pink-footed goose (N = 40). Figure S1. Ratios of genotype calls between the three different pipelines for devils and geese. Figure S2. Venn diagram depicting number of shared loci between the three different pipelines for (a) devil and (b) goose. Figure S3. PCoA of the devil dataset only for the three pipelines, considering all three populations. Row one shows data processed with a call rate of 70%, row two shows data processed less stringently with a call rate of 30%. Figure S4. PCoAs of the two datasets after processing through three pipelines filtered less stringently, allowing more missing data (30% call rate). Figure S5. a) Gel image example of sample quality from 1 (highest) to 8 (no apparent DNA); b) - d) Gel quality rank (rank 7 and 8 not included as too low quality to include in study) vs. the amount of missing data of a sample for the b) Stacks, c) SAMtools and d) GATK pipelines. (ZIP 346 kb)
DOI: 10.6084/m9.figshare.8222162
title: Additional file 2: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

description: Custom R script. (TXT 17 kb)
DOI: 10.6084/m9.figshare.8222156.v1
title: Additional file 1: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

description: Supplementary Methods: Tasmanian devil reduced-representation sequencing. Table S1. Summary statistics for the resultant SNP loci datasets of three pipelines, filtered less stringently at a higher allowable missing data (30% call rate; cf Table 1), for Tasmanian devil (N = 131) and pink-footed goose (N = 40). Figure S1. Ratios of genotype calls between the three different pipelines for devils and geese. Figure S2. Venn diagram depicting number of shared loci between the three different pipelines for (a) devil and (b) goose. Figure S3. PCoA of the devil dataset only for the three pipelines, considering all three populations. Row one shows data processed with a call rate of 70%, row two shows data processed less stringently with a call rate of 30%. Figure S4. PCoAs of the two datasets after processing through three pipelines filtered less stringently, allowing more missing data (30% call rate). Figure S5. a) Gel image example of sample quality from 1 (highest) to 8 (no apparent DNA); b) - d) Gel quality rank (rank 7 and 8 not included as too low quality to include in study) vs. the amount of missing data of a sample for the b) Stacks, c) SAMtools and d) GATK pipelines. (ZIP 346 kb)
DOI: 10.6084/m9.figshare.8222162.v1
title: Additional file 2: of From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

description: Custom R script. (TXT 17 kb)
DOI: 10.6084/m9.figshare.8222138
title: Additional file 2: of Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

description: Table S2. Single Nucleotide Polymorphsim genotypes after merging WVSU (Nimmakayala et al. 2016) and IBMCP (current work) data. (XLSX 5578 kb)
DOI: 10.6084/m9.figshare.8222138.v1
title: Additional file 2: of Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

description: Table S2. Single Nucleotide Polymorphsim genotypes after merging WVSU (Nimmakayala et al. 2016) and IBMCP (current work) data. (XLSX 5578 kb)
DOI: 10.6084/m9.figshare.8222135
title: Additional file 1: of Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

description: Table S1. Details of the accessions analysed in the current study. Group, subspecies and type are according passport data. MDS group is according MDS analysis (nd, ungruped). The assay indicates the origin of the data: WVSU (Nimmakayala et al. 2016), IBMCP (current work). (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8222126
title: Additional file 8: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S5. Module disease specificity. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.8222132
title: Additional file 9: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S6. Evidence for FOS/JUN transcription factor binding sites in lncRNA promoters of module 7. (a) Weeder motif scores. (b) Frequency matrix associated with top scoring motif (ATGAGTCATA). (c) Presence of top-scoring motif in ME7 lncRNAs. (d) Top 6 JASPAR database matches with top matrix hit (human-derived motifs only). (XLSX 56 kb)
DOI: 10.6084/m9.figshare.8222132.v1
title: Additional file 9: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S6. Evidence for FOS/JUN transcription factor binding sites in lncRNA promoters of module 7. (a) Weeder motif scores. (b) Frequency matrix associated with top scoring motif (ATGAGTCATA). (c) Presence of top-scoring motif in ME7 lncRNAs. (d) Top 6 JASPAR database matches with top matrix hit (human-derived motifs only). (XLSX 56 kb)
DOI: 10.6084/m9.figshare.8222135.v1
title: Additional file 1: of Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

description: Table S1. Details of the accessions analysed in the current study. Group, subspecies and type are according passport data. MDS group is according MDS analysis (nd, ungruped). The assay indicates the origin of the data: WVSU (Nimmakayala et al. 2016), IBMCP (current work). (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8222126.v1
title: Additional file 8: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S5. Module disease specificity. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.8222114
title: Additional file 6: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S3. Eigen-lnc coefficients (PC-MA scores) contributed by each protein coding gene. (XLSX 4910 kb)
DOI: 10.6084/m9.figshare.8222123
title: Additional file 7: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S4. ToppGene functional enrichment in pro-module protein coding genes. (XLSX 200 kb)
DOI: 10.6084/m9.figshare.8222123.v1
title: Additional file 7: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S4. ToppGene functional enrichment in pro-module protein coding genes. (XLSX 200 kb)
DOI: 10.6084/m9.figshare.8222111
title: Additional file 5: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S2. Module assignment and correlation of lncRNA association score profiles with the eigen-lncs. (XLSX 589 kb)
DOI: 10.6084/m9.figshare.8222114.v1
title: Additional file 6: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S3. Eigen-lnc coefficients (PC-MA scores) contributed by each protein coding gene. (XLSX 4910 kb)
DOI: 10.6084/m9.figshare.8222108
title: Additional file 4: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S1. Number of TCGA patients contributing to this study across 32 cancer types. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8222111.v1
title: Additional file 5: of Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

description: Table S2. Module assignment and correlation of lncRNA association score profiles with the eigen-lncs. (XLSX 589 kb)