Journal: bioRxiv

Article Title: Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden

doi: 10.1101/2024.04.10.588794

Figure Lengend Snippet: a, Experimental scheme for the in-vitro induction of senescence using Doxorubicin (DOXO) in five different cell types. b, Differential expression results of mRNA and microRNA profiling in five different human primary cell types. The table lists the number of mRNAs and microRNAs, respectively, which were included for DEA and that were differentially up- or downregulated (FDR < 0.15). c, Unsupervised heatmap clustering using RPM values for mRNA and microRNA expression. The top 3000 mRNAs and top 300 microRNAs according to CV% were used to prepare heatmaps. Pearson correlation was used for clustering of samples (columns) and mRNAs/microRNAs (rows). d, Differentially expressed mRNAs and microRNAs were compared between cell types and used for VENN analysis. e – f, mRNAs and microRNAs commonly regulated in four out of five senescent cell types were used for creating correlation networks, microRNA-mRNA pairs correlated with an adjusted p value < 0.01 were used for network construction. e, The upper network shows correlations between upregulated microRNAs and downregulated mRNAs, the lower network in f, shows correlations between downregulated microRNAs and upregulated mRNAs. For both analyses, all mRNAs in the respective networks were used for GO term enrichment using the category ‘Biological Process’. The Top 20 terms (FDR < 0.1) are shown.

Article Snippet: mRNA sequencing data were processed as recommended by Lexogen.

Techniques: In Vitro, Quantitative Proteomics, Expressing

Journal: bioRxiv

Article Title: Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden

doi: 10.1101/2024.04.10.588794

Figure Lengend Snippet: a, MA plots of miRNA expression in all five cell types. b, MA plots of mRNA expression in all five senescent cell types. Differentially expressed (FDR < 0.15) miRNAs and mRNAs respecrtively are highlighted in green.

Article Snippet: mRNA sequencing data were processed as recommended by Lexogen.

Techniques: Expressing

Journal: bioRxiv

Article Title: Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden

doi: 10.1101/2024.04.10.588794

Figure Lengend Snippet: a, Heatmaps on uniquely up- and downregulated (FDR < 0.15) miRNAs in individual senescent cell types. b, Heatmaps on uniquely up- or downregulated (FDR < 0.15) mRNAs in individual senescent cell types. For all heatmaps, row annotations specify the senescent cell type of the respective uniquely regulated miRNA/mRNA set.

Article Snippet: mRNA sequencing data were processed as recommended by Lexogen.

Techniques:

Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Comparative analysis of genome assemblies of Neospora caninum and Toxoplasma gondii using third-generation sequencing data reveals misassembly and karyotype differences. ( A ) Comparative analysis of the T. gondii type II ( Tg ME49) genome assembly and the N. caninum Liverpool ( Nc Liv) strain genome assembly, obtained based on Sanger technology sequencing data. ( B ) Comparative alignment of the Nc Liv genome assemblies using Sanger and third-generation (long-read) technology. ( C ) Comparative alignment of the T. gondii type II ( Tg ME49) genome assemblies based on Sanger technology sequencing data or third-generation (long-read) technology of T. gondii type I ( Tg RH). ( D ) Comparative alignment of the T. gondii type I ( Tg RH) and the Nc Liv genome assemblies based on third-generation (long-read) sequencing technology. ( E ) Chromosomal layout of N. caninum . Karyotype, chromosome length, telomeres, putative centromeres, and large repeats are shown.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques: Sequencing

Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Regions of synteny breaks between N. caninum and T. gondii are populated by three conserved domains. ( A ) Sequence identity of domains identified at regions where chromosomal rearrangements have occurred. ( B ) Graphical representation of Chromosome VIII of Nc Liv. Comparative alignment to the T. gondii chromosomes. Percentages of sequence identity are shown. Regions examined for the presence of motifs are indicated (light green). The position of the putative centromere is indicated in orange. Note that large repetitive regions were not identified in this chromosome. 5′ (light purple) and 3′ (dark purple) telomeres are indicated. The identity and number of domains found per region, in Chromosome VII, are indicated.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques: Sequencing

Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Comparative analysis of mitochondrial genome structures and annotations of Neospora and Toxoplasma reveals gene fragmentation and reshuffling between species and strains. ( A ) The repetitive nature of the gene structure in a 32-kb mitochondrial DNA contig of Nc Liv is graphically represented in a YASS plot. ( B ) The repetitive nature of the gene structure in a 16-kb mitochondrial DNA contig of Nc Liv is graphically represented in a YASS plot. ( C ) Comparative alignment between two Nc Liv mitochondrial contigs of 16 and 32 kb, respectively. ( D ) Comparative alignment between a Nc Liv mitochondrial contig of 32 kb and a Nc Uru1 mitochondrial contig of 38 kb. ( E ) Comparative alignment between two Nc Uru1 mitochondrial contigs of 16 and 38 kb, respectively. ( F ) The repetitive nature of the gene structure in a 16-kb mitochondrial DNA contig of Nc Uru1 is graphically represented in a YASS plot. ( G ) Comparative alignment between a Nc Liv mitochondrial contig of 32 kb and a T. gondii mitochondrial contigs of 39 kb.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques: