Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Differentially expressed miRNAs of EVs derived from serum of patients with leukaemia before irradiation vs. healthy donors. a Volcano plot; X axis: log2 transformed fold change; Y axis: −log10 transformed p -values. b Heatmap of upregulated and c heatmap of downregulated miRNAs in EVs from serum of patients with leukaemia. d Top 10 significant Kyoto Encyclopedia of Genes and Genomes database (KEGG) pathways affected by upregulated miRNAs of patients with leukaemia vs. healthy donors, ordered from top to bottom by p value, with the most significant pathway on the top. e Top 10 significant KEGG pathways affected by downregulated miRNAs of patients with leukaemia vs. healthy donors, ordered from top to bottom by p -value

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques: Derivative Assay, Irradiation, Transformation Assay

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Significantly up- ( n = 23) and downregulated ( n = 16) miRNAs in EVs from serum of patients with leukaemia vs. healthy volunteers

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Differentially expressed miRNAs of EVs derived from serum of patients with leukaemia after whole-body irradiation vs. before irradiation. a Volcano plot, b heatmap of upregulated and c heatmap of downregulated miRNAs in EVs from serum of patients with leukaemia after and before irradiation. d Top 10 KEGG pathways affected by upregulated miRNAs or e downregulated miRNAs from irradiated vs. non-irradiated patients with leukaemia

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques: Derivative Assay, Irradiation

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Significantly up- ( n = 11) and downregulated ( n = 15) miRNAs in EVs from serum of patients with leukaemia after irradiation

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Venn diagram analyses (program InteractiVenn, www.interactivenn.net ) of ( a ) upregulated or ( b ) downregulated miRNAs in AML, ALL and combined (AML+ALL = leukaemia) patients and of miRNAs ( c ) upregulated and ( d ) downregulated following TBI in AML, ALL and combined cohort patients (leukaemia)

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: Nature Genetics

Article Title: Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation

doi: 10.1038/s41588-024-01801-y

Figure Lengend Snippet: a . GSEA plot of Paneth cells from NWD1- vs. AIN76A-fed mice. The DSS signature significantly associates with the NWD1 diet (NES 2.99, Padj 2.5e-56). P value denote Benjamini-Hochberg adjusted value of the two-sided enrichment P-value from GSEA. b . Bar plot showing pathways elevated (P < 0.05, NES > 0.5) in Paneth cells from NWD1- when compared to AIN76A-fed animals. c . Prediction scores for Paneth (left) and goblet (right) cells on UMAP embedding from the scATAC data (Choi et al. ). d . Unsupervised clustering reveals two distinct clusters (c5, c20) that include Paneth cells. e. Bar plot listing gene ontology (GO) results based on differential peaks from the diet responsive Paneth cells. Pvalues were obtained from the EnrichR GO analysis and denote the results of Fisher’s exact test f . Immunofluorescence imaging of WGA and Olf4m showing intestinal crypts from mice fed with AIN/NWD1 diets. Asterisks earmark double positive cells. Scale bar indicates 10 µm.

Article Snippet: The intestinal epithelia of mice fed with control (AIN-76A) and western-style diets (3 months) were collected and sent for 10X Genomics scATAC sequencing analysis ( n = 2 mice per group) .

Techniques: Immunofluorescence, Imaging

Journal: Nature Genetics

Article Title: Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation

doi: 10.1038/s41588-024-01801-y

Figure Lengend Snippet: a , Schematics of the experimental approach designed to investigate the consequences of short- and long-term exposure to a western-style diet (NWD1) versus control (AIN-76A) diets. b , Heatmap showing z -scored DSS signature (DSS versus control; P adj < 0.05, log 2 -transformed fold change > 0.25) in PCs exposed to DSS or NWD1. c , Organoid multiplicities derived either from single ISCs or PCs, and from reconstituted doublets (L, Lgr5 + ISCs; P, PCs). Pooled data from n = 4 independent experiments. P values were calculated using one-way ANOVA and Tukey’s tests for group comparisons. Error bars depict s.d. d , Representative image of lineage tracings from a NWD1-fed Lyz1 -YFP mouse. Scale bars, 50 μm. The P value depicts the result of a two-sided Student’s t -test and the error bars represent s.d. Data from n = 3 mice. e , UMAP showing PCs from mice fed AIN-76A (AIN) and NWD1 ( n = 3 mice per condition). The DSS signature portrayed on UMAP embedding highlights a subcluster of PCs responsive to the NWD1 diet. f , Violin plots showing different levels of the DSS signature (top) and CytoTRACE score (bottom) between PCs responsive to the NWD1 diet and other PCs. P values show the significance of a two-sided Wilcoxon test. g , Violin plots representing marker genes of PCs responsive to the NWD1 diet, showing coexpression of stem and secretory markers. h , Heatmap visualization of GSVA, indicating pathways that are activated in PCs after exposure to DSS or NWD1. Comparison with data from ref. . i , UMAP plot of PC subset in the scATAC dataset of mice treated with AIN ( n = 2) and NWD1 ( n = 2). j , Heatmap listing differential peaks between diet response PCs and other PCs. k , Ideogram displaying the distribution along the mouse chromosomes (Chr) of the differential peaks observed upon diet response (red) when compared with those characteristic of PCs (blue).

Article Snippet: The intestinal epithelia of mice fed with control (AIN-76A) and western-style diets (3 months) were collected and sent for 10X Genomics scATAC sequencing analysis ( n = 2 mice per group) .

Techniques: Western Blot, Control, Transformation Assay, Derivative Assay, Marker, Comparison

Journal: Nature Genetics

Article Title: Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation

doi: 10.1038/s41588-024-01801-y

Figure Lengend Snippet: a . UMAP plot displaying 1 Mb processed scATAC data of the human colon (Becker et al. ). b , c . Average number of passenger mutations ( b ) in IBD-related and sporadic colon cancers N = 257 sCRCs and N = 25 IBD-CRCs. ( c ). Relative mutation frequency in IBD-enriched (N = 78) and sCRC-enriched (N = 136) bins based on two-sided Wilcox test (P < 0.01). Error bars are displayed from the mean and indicate the standard error from bootstrap with a 95% confidence interval. d . Barplot showing the genomic overview of differential bins across chromosomes. e. Boxplots relative to the gene set variation analysis (GSVA) scores of tumors stratified according to their predicted cell of origin. P values denote results of t tests. N = 27 Stem-predicted and N = 10 Goblet-predicted CRCs. Boxplots display the median, lower and upper hinges correspond to the first and third quartiles. Whiskers extend from the hinges to max/min values, no further than 1.5*inter-quartile range.

Article Snippet: The intestinal epithelia of mice fed with control (AIN-76A) and western-style diets (3 months) were collected and sent for 10X Genomics scATAC sequencing analysis ( n = 2 mice per group) .

Techniques: Mutagenesis

Journal: The Pharmacogenomics Journal

Article Title: A TOMM40 variable-length polymorphism predicts the age of late-onset Alzheimer's disease

doi: 10.1038/tpj.2009.69

Figure Lengend Snippet: Schematic overview of the TOMM40-APOE locus. ( a ) Genomic locations of the TOMM40 and APOE genes on chromosome 19 between 50 084 480 and 50 107 480 bp. The regions subjected to primary sequencing and phylogenetic analysis for the exploratory (R1) (23 kb) and confirmatory (R2) (10 kb) studies are highlighted on the genomic map (NCBI Build 36.3). ( b ) Distribution of SNP and insertion/deletion polymorphisms are shown on the gene structure of TOMM40 covered in the region that was subjected to primary sequencing. The region covers exons 6–10 and all associated intronic regions. The variable poly-T repeat (rs10524523) that is significantly associated with LOAD age of onset is depicted with the square labeled ‘P'.

Article Snippet: A proprietary sequencing analysis program called ‘Agent' (developed by Celera, Alameda, CA, USA) was used to align sequencing reads to the appropriate reference sequence, and produce ‘contigs' associated with each clone.

Techniques: Sequencing, Labeling