cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3643217_d6.v2
title: Additional file 9: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of gene sets from C2: Curated Gene Sets and C6: Oncogenic Signatures gene sets ( http://www.broadinstitute.org/gsea/msigdb/collections.jsp ) significantly enriched in MCF-7-Snail or MCF-7-Control phenotypes. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3643217_d8.v1
title: Additional file 7: of 
                     Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of differentially expressed genes between MCF-7-Snail and MCF-7-Control cells known to MetaCore knowledgebase to be directly transcriptionally regulated by c-Myc. (XLS 610 kb)
DOI: 10.6084/m9.figshare.c.3643217_d9.v1
title: Additional file 4: of 
                     Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 7602 unique annotated genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLSX 178 kb)
DOI: 10.6084/m9.figshare.c.3643217_d8.v2
title: Additional file 7: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of differentially expressed genes between MCF-7-Snail and MCF-7-Control cells known to MetaCore knowledgebase to be directly transcriptionally regulated by c-Myc. (XLS 610 kb)
DOI: 10.6084/m9.figshare.c.3643217_d9.v2
title: Additional file 4: of Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity

description: List of 7602 unique annotated genes differentially expressed between MCF-7-Snail and MCF-7-Control cells. (XLSX 178 kb)
DOI: 10.6084/m9.figshare.c.3643220_d2.v1
title: Additional file 3: Table S1. of A clone-free, single molecule map of the domestic cow (Bos taurus) genome

description: Tabulation of discordances between BtOM1.0 and UMD3.1. (XLSX 399Â kb)
DOI: 10.6084/m9.figshare.c.3643220_d4.v1
title: Additional file 4: Table S2. of A clone-free, single molecule map of the domestic cow (Bos taurus) genome

description: Tabulation of discordances between BtOM1.0 and Btau4.6. (XLSX 625Â kb)
DOI: 10.6084/m9.figshare.c.3643268_d3.v1
title: Additional file 4: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

description: Comparison of the frequency of select mutational events in breast cancer tumours versus cell lines. Differences in mutational frequencies of selected genes in TCGA BRCA tumours (n = 503) and CCLE breast cancer cell lines (n = 31). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3643268_d1.v1
title: Additional file 3: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

description: Top 1 % of differentially expressed genes between tumours and cell lines after filtering out genes correlated with stromal and immune scores in tumours (absolute tumour stromal and immune scores, Pearson correlation coefficient &lt;0.2, adjusted p values by t test). (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3643268_d2.v1
title: Additional file 2: of Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

description: Top 1 % of differentially expressed genes between tumours and cell lines (with adjusted p values by t test). (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3643274_d1.v1
title: Additional file 2: of Validation of the Dutch language version of the Safety Attitudes Questionnaire (SAQ-NL)

description: Research Dataset. (XLSX 687 kb)
DOI: 10.6084/m9.figshare.c.3643277_d6.v1
title: Additional file 16: Figure S7. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: Aâ  C. KEGG Gene Ontology (GO) enrichment analysis of differentially expressed genes between the two conditions (W and C) showing the main enriched processes in both experimental conditions. (A) Biological process, (B) Cellular component (C) Molecular function. (ZIP 4695Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d4.v1
title: Additional file 14: Table S9. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: List of all differentially expressed hydrophobin genes. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d7.v1
title: Additional file 3: Table S3. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: Annotation of all unigenes from the R. microporus transcriptome. (XLSX 9519Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d8.v1
title: Additional file 6: Table S5. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: All differentially down-regulated genes during saprotrophic growth of R. microporus. (XLSX 1631Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d10.v1
title: Additional file 5: Table S4. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: All differentially up-regulated genes during saprotrophic growth of R. microporus. (XLSX 1547Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d9.v1
title: Additional file 13: Table S8. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: List of all differentially expressed ATPâ  Binding cassette (ABC) transporters. (XLSX 394Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d12.v1
title: Additional file 7: Table S6. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: List of all differentially expressed Carbohydrate-active enzymes [Glycoside Hydrolase (GH), Glycosyltransferase (GT), Carbohydrate esterase (CE) and Polysaccharide lyase (PL) families]. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.c.3643277_d13.v1
title: Additional file 10: Table S7. of 
                     De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

description: List of all differentially expressed genes involved in Lignin degradation. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3643319_d6.v1
title: MOESM2 of Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits

description: Additional file 2. AF2_QUALsim.
DOI: 10.6084/m9.figshare.c.3643322_d1.v1
title: Additional file 1 of Design and engineering of a transmissible antiviral defense

description: Original data file used to generate estimates in Table 2.
DOI: 10.6084/m9.figshare.c.3643322_d2.v1
title: Additional file 2 of Design and engineering of a transmissible antiviral defense

description: Mathematica file used to generate Fig. 4d. Changes in parameters and initial densities are needed to generate the other panels.
DOI: 10.6084/m9.figshare.c.3643328_d1.v1
title: Additional file 1: of Training tomorrowâ  s leaders in global health: impact of the Afya Bora Consortium Fellowship on the careers of its alumni

description: Afya Bora Alumni Impact Survey: Survey used in this assessment. (CSV 1 kb)
DOI: 10.6084/m9.figshare.c.3643331_d1.v1
title: Additional file 4: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Raw MS data from sugarcane culms using Method 2, biological replicate2. (XLS 1.39 MB)
DOI: 10.6084/m9.figshare.c.3643331_d4.v1
title: Additional file 5: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: CWPs identified in 2 month-old sugarcane culms. (XLSX 30.3 kb)
DOI: 10.6084/m9.figshare.c.3643331_d3.v1
title: Additional file 3: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Raw MS data from sugarcane culms using Method 2, biological replicate1. (XLS 2.33 MB)
DOI: 10.6084/m9.figshare.c.3643331_d5.v1
title: Additional file 7: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Important features identified by Volcano plot. (XLSX 10.0 kb)
DOI: 10.6084/m9.figshare.c.3643331_d6.v1
title: Additional file 2: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Raw MS data from sugarcane culms using Method 1, biological replicate 2. (XLS 3.02 MB)
DOI: 10.6084/m9.figshare.c.3643331_d7.v1
title: Additional file 1: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Raw MS data from sugarcane culms using Method 1, biological replicate1. (XLS 2.26 MB)
DOI: 10.6084/m9.figshare.c.3643385_d1.v1
title: Additional file 4: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Per strain genotype concordance with HapMap. Total HapMap positions available for comparison with each strain and the corresponding number of concordant sites. (XLSX 4 kb)
DOI: 10.6084/m9.figshare.c.3643385_d2.v1
title: Additional file 3: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Pairwise variant comparisons. The number of SNPs and indels shared between any two strains contained in the MGP variation catalogue. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3643385_d3.v1
title: Additional file 5: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: VEP, GMS and SIFT annotations for SNPs and indels in each of the 13 strains. Total number of SNPs and indels annotated into each functional consequence predicted by VEP. Total number of SNPs with an estimated moderate (using GMS), radical (GMS), tolerated (using SIFT) and deleterious (SIFT) effect is also provided. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3643385_d5.v1
title: Additional file 7: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Candidate genes identified in the RF/J analysis. All genes which contained at least one missense SNP only found in the RF/J strain. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3643385_d7.v1
title: Additional file 6: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Private SNPs with multiple VEP consequences. Private SNPs with multiple predicted VEP consequences for each strain strain. Consequence predictions are based on gene models obtained from Ensembl 78. (TXT 66669 kb)
DOI: 10.6084/m9.figshare.c.3643385_d8.v1
title: Additional file 8: of Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations

description: Per strain over-represented pathways using genes containing private missense SNPs. For each strain separately significantly over-represented pathways were identified using only the genes which contained at least one private missense variant. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.c.3643397_d1.v1
title: Additional file 1: of Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure

description: Manhattan plot of the genome-wide association study for fatty acids in Nellore. The X-axis represents the chromosomes, and the Y-axis shows the proportion of genetic variance explained by windows of 10 adjacent SNPs in the following 18 fatty acids: arachidonic, CLA-cis, CLA-trans, docosahexaenoic, eicosatrienoic,myristoleic, MUFA, PUFA, myristic, n6:n3, oleic, omega-3, palmitic, stearic, palmitoleic and PUFA:SFA ratio in Nellore. (ZIP 1395Â kb)
DOI: 10.6084/m9.figshare.c.3643415_d10.v1
title: Additional file 4: Table S2. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Median and maximum focal F ST values from comparisons of each landrace population to all other landraces.
DOI: 10.6084/m9.figshare.c.3643415_d15.v1
title: Additional file 21: Table S10. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: 1,896 SNPs shared between wild barley and landrace populations.
DOI: 10.6084/m9.figshare.c.3643415_d19.v1
title: Additional file 15: Table S7. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Frequency of alleles private to the wild present in each of the landrace populations. Private SNPs in wild barley that are present in the landraces, including linkage group and their frequency in each landrace population.
DOI: 10.6084/m9.figshare.c.3643415_d18.v1
title: Additional file 19: Table S9. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Proportion of individuals involved in IBS segments (30 SNP each) between each landrace population and the 277 wild barley lines.
DOI: 10.6084/m9.figshare.c.3643415_d20.v1
title: Additional file 7: Table S3. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Chromosome painting. Individual landrace ancestry inferred at each genomic region. The cells are colored according to their inferred ancestry from the wild populations. Two haplotypes (rows) per landrace accession are depicted.
DOI: 10.6084/m9.figshare.c.3643421_d2.v1
title: Additional file 15: of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Generation of control recombination positive dataset. Two types of recombination events were introduced to simulated sequences: gene conversion and homologous recombination (reciprocal exchange). For gene conversion recombination, a subsequence from a randomly chosen donor gene is extracted, and used to replace the homologous subsequence in a randomly chosen recipient gene. For homologous recombination (reciprocal exchange), homologous subsequences from two randomly chosen genes are extracted and exchanged. Normal distribution is used to model the length of the recombination region. Exponential distribution is used to model the number of recombination events per gene. Exponential distribution with probability density function y = 0.52622e − 0.52622x is a good approximation of the distribution of frequency of number of recombination events per gene observed in our preliminary analysis. A custom perl program script was used to introduce multiple recombination events in a single dataset. The perl script takes 4 parameters, percentage of Gene conversion recombination“g%”, total recombination gene number “n”, recombination region mean length, “l” and standard deviation of recombination region length, “std”. The program randomly chose g% of the genes to introduce recombination into. For each recombinant gene, the program sampled the exponential distribution described above to determine the number of recombination events to introduce into the gene. For each recombination event, g% probability to introduce gene conversion event, and 1-g% probability to introduce homologous recombination events (reciprocal exchange), the length of recombination event was sampled from the normal distribution (l, std2). (ZIP 23 kb)
DOI: 10.6084/m9.figshare.c.3643421_d1.v1
title: Additional file 7: Table S3. of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Alignment and Analysis of TcTS Architectures. (a) Of the 3209 TcTS sequences in this study, 3176 contained at least 1 motif with an e-value of 1e-01 as determined by the described MEME analysis. The architectures, the in-order sequence of motifs, of each TcTS sequence were extracted and aligned as described. (b) Confidence heat map. Top row contains the motif numbers of the “model” TcTS architecture, where the model is determined by choosing the motif that is most frequent over all TcTS at each position. The cells are colored red if the model motif at that position is found in &gt;1000 sequences, black for motifs preceding the signal peptide sequence or in the hyper-variable region containing SAPA repeats, and blue otherwise. The 2nd row displays a bar-graph of the minimum smoothed entropy for the motif region. The remainder of the table is color-coded according to the “confidence score” of the motif-to-architecture for each cell. The confidence score is calculated as: (-1 * loge(MEME e-value))1.5 and the colors range from white (low) to blue (mid) to red (high). Note that the score reflects the assigned motif at each position regardless of whether it matches the model. (XLSX 1439 kb)
DOI: 10.6084/m9.figshare.c.3643421_d3.v1
title: Additional file 11: Table S5. of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Recombination events. a) Detailed information of 2087 recombination events detected in TcTS gene family. b) Summary of number and percentage of newly annotated TcTS and previously annotated TcTS participating in recombination events as recombinant product, major donor or minor donor. (XLSX 549 kb)
DOI: 10.6084/m9.figshare.c.3643421_d7.v1
title: Additional file 5: Table S2. of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Proteomic Confirmation of TcTS. (a) Summary of proteomic analysis. The “Min” value represents the minimum number of proteins (and their peptides) that could account for all identified peptides (see “TOP PROTEIN” in b and c), while the “Max” value is the total number of proteins (and their peptides) that contain the identified peptides (e.g. isoforms and related proteins). (b) List of all identified TcTS proteins. (c) List of identified newly identified TcTS proteins. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3643421_d8.v1
title: Additional file 16: of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Motif and MEME scripts. (RAR 42 kb)
DOI: 10.6084/m9.figshare.c.3643445_d1.v1
title: Additional file 3: Table S3. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

description: WebGestalt Disease enrichment analysis of the set of unique DEX-regulated genes (n = 139) with TSS near epigenetic clock CpGs. For the primary analysis, we used as reference the set of genes expressed above background in our peripheral blood gene expression arrays. This analysis was repeated using a more condensed background comprised only of the genes neighboring 21 K CpGs that showed DEX-induced mRNA expression changes (n = 5,443). While this post-hoc analysis yielded no statistically significant results after correction for multiple testing (P values presented in the last column), the top 10 diseases were very similar (with higher but nominally significant P values for the top three hits) with the analysis using the broader reference set of genes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3643445_d2.v1
title: Additional file 2: Table S2. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

description: Annotation of genes with transcription start sites (TSS) near epigenetic clock CpGs and their expression changes in response to DEX. Gene annotation was based on [43]. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3643445_d3.v1
title: Additional file 1: Table S1. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

description: Location of epigenetic clock CpGs in relation to the nearest glucocorticoid response element (as shown by within GR ChIP-Seq peaks in a lymphoblastoid cell line) and their methylation changes in response to the glucocorticoid receptor agonist dexamethasone. (DEX). (XLSX 68 kb)
DOI: 10.6084/m9.figshare.c.3643451_d1.v1
title: Additional file 2: Table S2. of A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax)

description: Detailed positions of individual SNPs in the constructed genetic map. (CSV 281 kb)
DOI: 10.6084/m9.figshare.c.3643451_d2.v1
title: Additional file 1: Table S1. of A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax)

description: Origin of samples and barcodes. This file provides details for each sample used i.e., sample ID, family, gender, barcode used, number of raw reads paired-ended and number of RAD-tags. (CSV 23 kb)
DOI: 10.6084/m9.figshare.c.3643469_d1.v1
title: Additional file 1: of Pharmacokinetics (PK), pharmacodynamics (PD), and PK-PD integration of ceftiofur after a single intravenous, subcutaneous and subcutaneous-LA administration in lactating goats

description: Plasma Ceftiofur concentrations and time kill curves data. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3643472_d1.v1
title: Additional file 1 of Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

description: Table with expression fold changes and p-values. Excel file with all expression FPKM values for all genes, fold changes and FDR corrected p-values for all genes that were found to be significantly differentially expressed in at least one comparison. The file also includes the assignments of genes to expression biclusters. (XLS 19558 kb)
DOI: 10.6084/m9.figshare.c.3643475_d1.v1
title: Additional file 2: of Bifidobacteria grown on human milk oligosaccharides downregulate the expression of inflammation-related genes in Caco-2 cells

description: A Microsoft Excel file that contains spreadsheets of Caco-2 genes differentially expressed in response to B. breve grown on GLU, LAC, or HMO. (XLSX 177 kb)
DOI: 10.6084/m9.figshare.c.3643475_d2.v1
title: Additional file 1: of Bifidobacteria grown on human milk oligosaccharides downregulate the expression of inflammation-related genes in Caco-2 cells

description: A Microsoft Excel file that contains spreadsheets of Caco-2 genes differentially expressed in response to B. infantis grown on GLU, LAC, or HMO. (XLSX 86 kb)